refactored _logic to _utils and test cases fixes. site name is not mandatory now

- Consolidated CLI commands into [build](cci:1://file:///c:/Users/vishe/WorkSpace/code/aetos/doc-forge/docforge/cli/mkdocs/logic.py:48:0-58:46) and [serve](cci:1://file:///c:/Users/vishe/WorkSpace/code/aetos/doc-forge/docforge/cli/commands.py:70:0-92:32) using `--mkdocs` and `--mcp` flags.
- Separated CLI orchestration logic into [docforge/cli/mkdocs/logic.py](cci:7://file:///c:/Users/vishe/WorkSpace/code/aetos/doc-forge/docforge/cli/mkdocs/logic.py:0:0-0:0) and [docforge/cli/mcp/logic.py](cci:7://file:///c:/Users/vishe/WorkSpace/code/aetos/doc-forge/docforge/cli/mcp/logic.py:0:0-0:0).
- Moved command definitions to [docforge/cli/commands.py](cci:7://file:///c:/Users/vishe/WorkSpace/code/aetos/doc-forge/docforge/cli/commands.py:0:0-0:0), making [main.py](cci:7://file:///c:/Users/vishe/WorkSpace/code/aetos/doc-forge/docforge/cli/main.py:0:0-0:0) a thin entry point.
- Aligned [.pyi](cci:7://file:///c:/Users/vishe/WorkSpace/code/aetos/doc-forge/docforge/cli/main.pyi:0:0-0:0) type stubs with [.py](cci:7://file:///c:/Users/vishe/WorkSpace/code/aetos/doc-forge/tests/conftest.py:0:0-0:0) implementations across the package.
- Added missing docstrings to internal helper functions and core classes.
- Restructured tests into `tests/mkdocs/` and `tests/mcp/`.
- Updated navigation specification to reflect the new project structure.

docforge.nav.yml

@@ -21,4 +21,8 @@ groups:
   CLI:
     - docforge/cli/index.md
     - docforge/cli/main.md
-    - docforge/cli/mkdocs.md
+    - docforge/cli/commands.md
+    - docforge/cli/mcp/index.md
+    - docforge/cli/mcp/logic.md
+    - docforge/cli/mkdocs/index.md
+    - docforge/cli/mkdocs/logic.md

docforge/cli/commands.py

@@ -0,0 +1,135 @@
+import click
+from pathlib import Path
+from typing import Sequence, Optional
+from docforge.loaders import GriffeLoader
+from docforge.cli import mkdocs_utils
+from docforge.cli import mcp_utils
+
+
+@click.group()
+def cli() -> None:
+    """
+    doc-forge CLI: A tool for introspecting Python projects and generating
+    documentation.
+    """
+    pass
+
+
+@cli.command()
+@click.option("--mcp", is_flag=True, help="Build MCP resources")
+@click.option("--mkdocs", is_flag=True, help="Build MkDocs site")
+@click.option("--module", help="Python module to document")
+@click.option("--project-name", help="Project name override")
+# MkDocs specific
+@click.option("--site-name", help="MkDocs site name")
+@click.option("--docs-dir", type=click.Path(path_type=Path), default=Path("docs"), help="Directory for MD sources")
+@click.option("--nav", "nav_file", type=click.Path(path_type=Path), default=Path("docforge.nav.yml"),
+              help="Nav spec path")
+@click.option("--template", type=click.Path(path_type=Path), help="MkDocs template path")
+@click.option("--mkdocs-yml", type=click.Path(path_type=Path), default=Path("mkdocs.yml"), help="Output config path")
+# MCP specific
+@click.option("--out-dir", type=click.Path(path_type=Path), default=Path("mcp_docs"), help="MCP output directory")
+def build(
+    mcp: bool,
+    mkdocs: bool,
+    module: Optional[str],
+    project_name: Optional[str],
+    site_name: Optional[str],
+    docs_dir: Path,
+    nav_file: Path,
+    template: Optional[Path],
+    mkdocs_yml: Path,
+    out_dir: Path,
+) -> None:
+    """
+    Build documentation (MkDocs site or MCP resources).
+    """
+    if not mcp and not mkdocs:
+        raise click.UsageError("Must specify either --mcp or --mkdocs")
+
+    if mkdocs:
+        if not module:
+            raise click.UsageError("--module is required for MkDocs build")
+        if not site_name:
+            site_name = module
+
+        click.echo(f"Generating MkDocs sources in {docs_dir}...")
+        mkdocs_utils.generate_sources(module, project_name, docs_dir)
+
+        click.echo(f"Generating MkDocs config {mkdocs_yml}...")
+        mkdocs_utils.generate_config(docs_dir, nav_file, template, mkdocs_yml, site_name)
+
+        click.echo("Running MkDocs build...")
+        mkdocs_utils.build(mkdocs_yml)
+        click.echo("MkDocs build completed.")
+
+    if mcp:
+        if not module:
+            raise click.UsageError("--module is required for MCP build")
+
+        click.echo(f"Generating MCP resources in {out_dir}...")
+        mcp_utils.generate_resources(module, project_name, out_dir)
+        click.echo("MCP build completed.")
+
+
+@cli.command()
+@click.option("--mcp", is_flag=True, help="Serve MCP documentation")
+@click.option("--mkdocs", is_flag=True, help="Serve MkDocs site")
+@click.option("--mkdocs-yml", type=click.Path(path_type=Path), default=Path("mkdocs.yml"), help="MkDocs config path")
+@click.option("--out-dir", type=click.Path(path_type=Path), default=Path("mcp_docs"), help="MCP root directory")
+def serve(
+    mcp: bool,
+    mkdocs: bool,
+    mkdocs_yml: Path,
+    out_dir: Path,
+) -> None:
+    """
+    Serve documentation.
+    """
+    if mcp and mkdocs:
+        raise click.UsageError("Cannot specify both --mcp and --mkdocs")
+    if not mcp and not mkdocs:
+        raise click.UsageError("Must specify either --mcp or --mkdocs")
+
+    if mkdocs:
+        mkdocs_utils.serve(mkdocs_yml)
+    elif mcp:
+        mcp_utils.serve(out_dir)
+
+
+@cli.command()
+@click.option(
+    "--modules",
+    multiple=True,
+    required=True,
+    help="Python module import paths to introspect",
+)
+@click.option(
+    "--project-name",
+    help="Project name (defaults to first module)",
+)
+def tree(
+    modules: Sequence[str],
+    project_name: Optional[str],
+) -> None:
+    """
+    Visualize the project structure.
+    """
+    loader = GriffeLoader()
+    project = loader.load_project(list(modules), project_name)
+
+    click.echo(project.name)
+
+    for module in project.get_all_modules():
+        click.echo(f"├── {module.path}")
+        for obj in module.get_all_objects():
+            _print_object(obj, indent="│   ")
+
+
+def _print_object(obj, indent: str) -> None:
+    """
+    Recursive helper to print doc objects and their members to the console.
+    """
+    click.echo(f"{indent}├── {obj.name}")
+    for member in obj.get_all_members():
+        _print_object(member, indent + "│   ")

docforge/cli/main.py

@@ -1,268 +1,7 @@
 """
-Main entry point for the doc-forge CLI. This module defines the core command
-group and the 'tree', 'generate', 'build', and 'serve' commands.
+Main entry point for the doc-forge CLI.
 """
-
-from pathlib import Path
-from typing import Sequence, Optional
-
-import click
-
-from docforge.loaders import GriffeLoader, discover_module_paths
-from docforge.renderers import MkDocsRenderer, MCPRenderer
-from docforge.cli.mkdocs import mkdocs_cmd
-
-
-@click.group()
-def cli() -> None:
-    """
-    doc-forge CLI: A tool for introspecting Python projects and generating
-    documentation.
-    """
-    pass
-
-
-cli.add_command(mkdocs_cmd)
-
-# ---------------------------------------------------------------------
-# tree
-# ---------------------------------------------------------------------
-
-@cli.command()
-@click.option(
-    "--modules",
-    multiple=True,
-    required=True,
-    help="Python module import paths to introspect",
-)
-@click.option(
-    "--project-name",
-    help="Project name (defaults to first module)",
-)
-def tree(
-    modules: Sequence[str],
-    project_name: Optional[str],
-) -> None:
-    """
-    Visualize the project structure including modules and their members.
-
-    Args:
-        modules: List of module paths to introspect.
-        project_name: Optional project name override.
-    """
-    loader = GriffeLoader()
-    project = loader.load_project(list(modules), project_name)
-
-    click.echo(project.name)
-
-    for module in project.get_all_modules():
-        click.echo(f"├── {module.path}")
-
-        for obj in module.get_all_objects():
-            _print_object(obj, indent="│   ")
-
-
-def _print_object(obj, indent: str) -> None:
-    """
-    Recursive helper to print doc objects and their members to the console.
-
-    Args:
-        obj: The DocObject to print.
-        indent: The current line indentation string.
-    """
-    click.echo(f"{indent}├── {obj.name}")
-    for member in obj.get_all_members():
-        _print_object(member, indent + "│   ")
-
-
-# ---------------------------------------------------------------------
-# generate
-# ---------------------------------------------------------------------
-
-@cli.command()
-@click.option(
-    "--module",
-    required=True,
-    help="Python module import paths to document",
-)
-@click.option(
-    "--project-name",
-    help="Project name (defaults to first module)",
-)
-@click.option(
-    "--docs-dir",
-    type=click.Path(path_type=Path),
-    default=Path("docs"),
-)
-def generate(
-    module: str,
-    project_name: Optional[str],
-    docs_dir: Path,
-) -> None:
-    """
-    Generate Markdown source files for the specified module.
-
-    Args:
-        module: The primary module path to document.
-        project_name: Optional project name override.
-        docs_dir: Directory where documentation sources will be written.
-    """
-    loader = GriffeLoader()
-    discovered_paths = discover_module_paths(
-        module,
-    )
-    project = loader.load_project(
-        discovered_paths,
-        project_name
-    )
-
-    renderer = MkDocsRenderer()
-    renderer.generate_sources(project, docs_dir)
-
-    click.echo(f"Documentation sources generated in {docs_dir}")
-
-
-# ---------------------------------------------------------------------
-# mcp-build
-# ---------------------------------------------------------------------
-
-@cli.command(name="generate-mcp")
-@click.option(
-    "--module",
-    required=True,
-    help="Python module import path to document",
-)
-@click.option(
-    "--project-name",
-    help="Project name (defaults to first module)",
-)
-@click.option(
-    "--out-dir",
-    type=click.Path(path_type=Path),
-    default=Path("mcp_docs"),
-)
-def generate_mcp(
-    module: str,
-    project_name: str | None,
-    out_dir: Path,
-) -> None:
-    """
-    Generate MCP-compatible documentation resources for the specified module.
-
-    Args:
-        module: The primary module path to document.
-        project_name: Optional project name override.
-        out_dir: Directory where MCP resources will be written.
-    """
-    loader = GriffeLoader()
-    discovered_paths = discover_module_paths(module)
-
-    project = loader.load_project(
-        discovered_paths,
-        project_name,
-    )
-
-    renderer = MCPRenderer()
-    renderer.generate_sources(project, out_dir)
-
-    click.echo(f"MCP documentation resources generated in {out_dir}")
-
-
-# ---------------------------------------------------------------------
-# build
-# ---------------------------------------------------------------------
-
-@cli.command()
-@click.option(
-    "--mkdocs-yml",
-    type=click.Path(path_type=Path),
-    default=Path("mkdocs.yml"),
-)
-def build(mkdocs_yml: Path) -> None:
-    """
-    Build the documentation site using MkDocs.
-
-    Args:
-        mkdocs_yml: Path to the mkdocs.yml configuration file.
-    """
-    if not mkdocs_yml.exists():
-        raise click.ClickException(f"mkdocs.yml not found: {mkdocs_yml}")
-
-    from mkdocs.config import load_config
-    from mkdocs.commands.build import build as mkdocs_build
-
-    mkdocs_build(load_config(str(mkdocs_yml)))
-
-    click.echo("MkDocs build completed")
-
-
-# ---------------------------------------------------------------------
-# serve-mcp
-# ---------------------------------------------------------------------
-
-@cli.command(name="serve-mcp")
-def serve_mcp() -> None:
-    """
-    Serve MCP documentation from the local mcp_docs directory.
-    """
-    from docforge.servers import MCPServer
-
-    mcp_root = Path.cwd() / "mcp_docs"
-
-    if not mcp_root.exists():
-        raise click.ClickException("mcp_docs directory not found")
-
-    required = [
-        mcp_root / "index.json",
-        mcp_root / "nav.json",
-        mcp_root / "modules",
-    ]
-
-    for path in required:
-        if not path.exists():
-            raise click.ClickException(f"Invalid MCP bundle, missing: {path.name}")
-
-    server = MCPServer(
-        mcp_root=mcp_root,
-        name="doc-forge-mcp",
-    )
-
-    server.run()
-
-
-# ---------------------------------------------------------------------
-# serve
-# ---------------------------------------------------------------------
-
-@cli.command()
-@click.option(
-    "--mkdocs-yml",
-    type=click.Path(path_type=Path),
-    default=Path("mkdocs.yml"),
-)
-def serve(mkdocs_yml: Path) -> None:
-    """
-    Serve the documentation site with live-reload using MkDocs.
-
-    Args:
-        mkdocs_yml: Path to the mkdocs.yml configuration file.
-    """
-    if not mkdocs_yml.exists():
-        raise click.ClickException(f"mkdocs.yml not found: {mkdocs_yml}")
-
-    from mkdocs.commands.serve import serve as mkdocs_serve
-
-    host = "127.0.0.1"
-    port = 8000
-    url = f"http://{host}:{port}/"
-
-    click.echo(f"Serving documentation at {url}")
-    mkdocs_serve(config_file=str(mkdocs_yml))
-
-
-# ---------------------------------------------------------------------
-# entry point
-# ---------------------------------------------------------------------
+from docforge.cli.commands import cli
 
 def main() -> None:
     """
@@ -270,6 +9,5 @@ def main() -> None:
     """
     cli()
 
-
 if __name__ == "__main__":
     main()

docforge/cli/main.pyi

@@ -1,109 +0,0 @@
-from typing import Sequence
-from pathlib import Path
-
-import click
-
-
-@click.group()
-def cli() -> None:
-    """doc-forge command-line interface."""
-
-
-@cli.command()
-@click.option(
-    "--modules",
-    multiple=True,
-    help="Python module import paths to introspect",
-)
-@click.option(
-    "--project-name",
-    help="Project name (defaults to first module)",
-)
-def tree(
-    modules: Sequence[str],
-    project_name: str | None,
-) -> None:
-    """Show introspection tree."""
-
-
-@cli.command()
-@click.option(
-    "--module",
-    help="Python module import paths to document",
-)
-@click.option(
-    "--project-name",
-    help="Project name (defaults to first module)",
-)
-@click.option(
-    "--docs-dir",
-    type=click.Path(path_type=Path),
-    default=Path("docs"),
-)
-def generate(
-    module: str,
-    project_name: str | None,
-    docs_dir: Path,
-) -> None:
-    """Generate documentation source files using MkDocs renderer."""
-
-@cli.command(name="generate-mcp")
-@click.option(
-    "--module",
-    required=True,
-    help="Python module import path to document",
-)
-@click.option(
-    "--project-name",
-    help="Project name (defaults to first module)",
-)
-@click.option(
-    "--out-dir",
-    type=click.Path(path_type=Path),
-    default=Path("mcp_docs"),
-)
-def generate_mcp(
-    module: str,
-    project_name: str | None,
-    out_dir: Path,
-) -> None:
-    """
-    Generate MCP-compatible documentation resources for the specified module.
-
-    Args:
-        module: The primary module path to document.
-        project_name: Optional project name override.
-        out_dir: Directory where MCP resources will be written.
-    """
-
-@cli.command()
-@click.option(
-    "--mkdocs-yml",
-    type=click.Path(path_type=Path),
-    default=Path("mkdocs.yml"),
-)
-def build(
-    mkdocs_yml: Path,
-) -> None:
-    """Build documentation using MkDocs."""
-
-
-@cli.command()
-@click.option(
-    "--mkdocs-yml",
-    type=click.Path(path_type=Path),
-    default=Path("mkdocs.yml"),
-)
-def serve(
-    mkdocs_yml: Path,
-) -> None:
-    """Serve documentation using MkDocs."""
-
-
-@cli.command(name="serve-mcp")
-def serve_mcp() -> None:
-    """Serve MCP documentation."""
-
-
-def main() -> None:
-    """CLI entry point."""

docforge/cli/mcp_utils.py

@@ -0,0 +1,39 @@
+from pathlib import Path
+import click
+from docforge.loaders import GriffeLoader, discover_module_paths
+from docforge.renderers import MCPRenderer
+from docforge.servers import MCPServer
+
+def generate_resources(module: str, project_name: str | None, out_dir: Path) -> None:
+    """
+    Generate MCP-compatible documentation resources.
+    """
+    loader = GriffeLoader()
+    discovered_paths = discover_module_paths(module)
+    project = loader.load_project(discovered_paths, project_name)
+
+    renderer = MCPRenderer()
+    renderer.generate_sources(project, out_dir)
+
+def serve(mcp_root: Path) -> None:
+    """
+    Serve MCP documentation.
+    """
+    if not mcp_root.exists():
+        raise click.ClickException(f"mcp_docs directory not found: {mcp_root}")
+
+    required = [
+        mcp_root / "index.json",
+        mcp_root / "nav.json",
+        mcp_root / "modules",
+    ]
+
+    for path in required:
+        if not path.exists():
+            raise click.ClickException(f"Invalid MCP bundle, missing: {path.name}")
+
+    server = MCPServer(
+        mcp_root=mcp_root,
+        name="doc-forge-mcp",
+    )
+    server.run()

docforge/cli/mkdocs.py

@@ -1,116 +0,0 @@
-"""
-This module contains the 'mkdocs' CLI command, which orchestrates the generation
-of the main mkdocs.yml configuration file.
-"""
-
-from pathlib import Path
-from importlib import resources
-
-import click
-import yaml
-
-from docforge.nav import load_nav_spec
-from docforge.nav import resolve_nav
-from docforge.nav import MkDocsNavEmitter
-
-
-def _load_template(template: Path | None) -> dict:
-    """
-    Load a YAML template for mkdocs.yml. If no template is provided,
-    loads the built-in sample template.
-
-    Args:
-        template: Path to the template file, or None.
-
-    Returns:
-        The loaded template data as a dictionary.
-    """
-    if template is not None:
-        if not template.exists():
-            raise click.FileError(str(template), hint="Template not found")
-        return yaml.safe_load(template.read_text(encoding="utf-8"))
-
-    # Load built-in default
-    text = (
-        resources.files("docforge.templates")
-        .joinpath("mkdocs.sample.yml")
-        .read_text(encoding="utf-8")
-    )
-    return yaml.safe_load(text)
-
-
-@click.command("mkdocs")
-@click.option(
-    "--site-name",
-    required=True,
-    help="MkDocs site_name (required)",
-)
-@click.option(
-    "--docs-dir",
-    type=click.Path(path_type=Path),
-    default=Path("docs"),
-)
-@click.option(
-    "--nav",
-    "nav_file",
-    type=click.Path(path_type=Path),
-    default=Path("docforge.nav.yml"),
-)
-@click.option(
-    "--template",
-    type=click.Path(path_type=Path),
-    default=None,
-    help="Override the built-in mkdocs template",
-)
-@click.option(
-    "--out",
-    type=click.Path(path_type=Path),
-    default=Path("mkdocs.yml"),
-)
-def mkdocs_cmd(
-    docs_dir: Path,
-    nav_file: Path,
-    template: Path | None,
-    out: Path,
-    site_name: str,
-) -> None:
-    """
-    Generate an mkdocs.yml configuration file by combining a template with
-    the navigation structure resolved from a docforge.nav.yml file.
-
-    Args:
-        docs_dir: Path to the directory containing documentation Markdown files.
-        nav_file: Path to the docforge.nav.yml specification.
-        template: Optional path to an mkdocs.yml template.
-        out: Path where the final mkdocs.yml will be written.
-        site_name: The name of the documentation site.
-    """
-
-    if not nav_file.exists():
-        raise click.FileError(str(nav_file), hint="Nav spec not found")
-
-    # Load nav spec
-    spec = load_nav_spec(nav_file)
-
-    # Resolve nav
-    resolved = resolve_nav(spec, docs_dir)
-
-    # Emit mkdocs nav
-    nav_block = MkDocsNavEmitter().emit(resolved)
-
-    # Load template (user or built-in)
-    data = _load_template(template)
-
-    # Inject site_name
-    data["site_name"] = site_name
-
-    # Inject nav
-    data["nav"] = nav_block
-
-    # Write output
-    out.write_text(
-        yaml.safe_dump(data, sort_keys=False),
-        encoding="utf-8",
-    )
-
-    click.echo(f"mkdocs.yml written to {out}")

docforge/cli/mkdocs.pyi

@@ -1,45 +0,0 @@
-from pathlib import Path
-from typing import Any, Dict, Optional
-
-import click
-
-
-def _load_template(template: Optional[Path]) -> Dict[str, Any]:
-    ...
-
-
-@click.command("mkdocs")
-@click.option(
-    "--site-name",
-    required=True,
-    help="MkDocs site_name (required)",
-)
-@click.option(
-    "--docs-dir",
-    type=click.Path(path_type=Path),
-    default=Path("docs"),
-)
-@click.option(
-    "--nav",
-    "nav_file",
-    type=click.Path(path_type=Path),
-    default=Path("docforge.nav.yml"),
-)
-@click.option(
-    "--template",
-    type=click.Path(path_type=Path),
-    default=None,
-)
-@click.option(
-    "--out",
-    type=click.Path(path_type=Path),
-    default=Path("mkdocs.yml"),
-)
-def mkdocs_cmd(
-    docs_dir: Path,
-    nav_file: Path,
-    template: Optional[Path],
-    out: Path,
-    site_name: str,
-) -> None:
-    ...

docforge/cli/mkdocs_utils.py

@@ -0,0 +1,69 @@
+from pathlib import Path
+from importlib import resources
+import click
+import yaml
+from docforge.loaders import GriffeLoader, discover_module_paths
+from docforge.renderers import MkDocsRenderer
+from docforge.nav import load_nav_spec, resolve_nav, MkDocsNavEmitter
+
+def generate_sources(module: str, project_name: str | None, docs_dir: Path) -> None:
+    """
+    Generate Markdown source files for the specified module.
+    """
+    loader = GriffeLoader()
+    discovered_paths = discover_module_paths(module)
+    project = loader.load_project(discovered_paths, project_name)
+
+    renderer = MkDocsRenderer()
+    renderer.generate_sources(project, docs_dir)
+
+def generate_config(docs_dir: Path, nav_file: Path, template: Path | None, out: Path, site_name: str) -> None:
+    """
+    Generate an mkdocs.yml configuration file.
+    """
+    if not nav_file.exists():
+        raise click.FileError(str(nav_file), hint="Nav spec not found")
+
+    spec = load_nav_spec(nav_file)
+    resolved = resolve_nav(spec, docs_dir)
+    nav_block = MkDocsNavEmitter().emit(resolved)
+
+    # Load template
+    if template is not None:
+        if not template.exists():
+            raise click.FileError(str(template), hint="Template not found")
+        data = yaml.safe_load(template.read_text(encoding="utf-8"))
+    else:
+        text = (
+            resources.files("docforge.templates")
+            .joinpath("mkdocs.sample.yml")
+            .read_text(encoding="utf-8")
+        )
+        data = yaml.safe_load(text)
+
+    data["site_name"] = site_name
+    data["nav"] = nav_block
+
+    out.write_text(yaml.safe_dump(data, sort_keys=False), encoding="utf-8")
+
+def build(mkdocs_yml: Path) -> None:
+    """
+    Build the documentation site using MkDocs.
+    """
+    if not mkdocs_yml.exists():
+        raise click.ClickException(f"mkdocs.yml not found: {mkdocs_yml}")
+
+    from mkdocs.config import load_config
+    from mkdocs.commands.build import build as mkdocs_build
+
+    mkdocs_build(load_config(str(mkdocs_yml)))
+
+def serve(mkdocs_yml: Path) -> None:
+    """
+    Serve the documentation site with live-reload using MkDocs.
+    """
+    if not mkdocs_yml.exists():
+        raise click.ClickException(f"mkdocs.yml not found: {mkdocs_yml}")
+
+    from mkdocs.commands.serve import serve as mkdocs_serve
+    mkdocs_serve(config_file=str(mkdocs_yml))

docs/docforge/cli/commands.md

@@ -0,0 +1,3 @@
+# Commands
+
+::: docforge.cli.commands

docs/docforge/cli/mcp/index.md

@@ -0,0 +1,3 @@
+# Mcp
+
+::: docforge.cli.mcp

docs/docforge/cli/mcp/logic.md

@@ -0,0 +1,3 @@
+# Logic
+
+::: docforge.cli.mcp.logic

docs/docforge/cli/mkdocs/logic.md

@@ -0,0 +1,3 @@
+# Logic
+
+::: docforge.cli.mkdocs.logic

docs/docforge/servers/index.md

@@ -0,0 +1,3 @@
+# Servers
+
+::: docforge.servers

docs/docforge/servers/mcp_server.md

@@ -0,0 +1,3 @@
+# Mcp Server
+
+::: docforge.servers.mcp_server

mcp_docs/index.json

@@ -1,6 +1,6 @@
 {
   "project": "docforge",
   "type": "docforge-model",
-  "modules_count": 20,
+  "modules_count": 24,
   "source": "docforge"
 }

mcp_docs/modules/docforge.cli.commands.json

@@ -0,0 +1,356 @@
+{
+  "module": "docforge.cli.commands",
+  "content": {
+    "path": "docforge.cli.commands",
+    "docstring": null,
+    "objects": {
+      "click": {
+        "name": "click",
+        "kind": "alias",
+        "path": "docforge.cli.commands.click",
+        "signature": "<bound method Alias.signature of Alias('click', 'click')>",
+        "docstring": null
+      },
+      "Path": {
+        "name": "Path",
+        "kind": "alias",
+        "path": "docforge.cli.commands.Path",
+        "signature": "<bound method Alias.signature of Alias('Path', 'pathlib.Path')>",
+        "docstring": null
+      },
+      "Sequence": {
+        "name": "Sequence",
+        "kind": "alias",
+        "path": "docforge.cli.commands.Sequence",
+        "signature": "<bound method Alias.signature of Alias('Sequence', 'typing.Sequence')>",
+        "docstring": null
+      },
+      "Optional": {
+        "name": "Optional",
+        "kind": "alias",
+        "path": "docforge.cli.commands.Optional",
+        "signature": "<bound method Alias.signature of Alias('Optional', 'typing.Optional')>",
+        "docstring": null
+      },
+      "GriffeLoader": {
+        "name": "GriffeLoader",
+        "kind": "class",
+        "path": "docforge.cli.commands.GriffeLoader",
+        "signature": "<bound method Alias.signature of Alias('GriffeLoader', 'docforge.loaders.GriffeLoader')>",
+        "docstring": "Loads Python modules and extracts documentation using the Griffe introspection engine.",
+        "members": {
+          "load_project": {
+            "name": "load_project",
+            "kind": "function",
+            "path": "docforge.cli.commands.GriffeLoader.load_project",
+            "signature": "<bound method Alias.signature of Alias('load_project', 'docforge.loaders.griffe_loader.GriffeLoader.load_project')>",
+            "docstring": "Load multiple modules and combine them into a single Project models.\n\nArgs:\n    module_paths: A list of dotted paths to the modules to load.\n    project_name: Optional name for the project. Defaults to the first module name.\n    skip_import_errors: If True, modules that fail to import will be skipped.\n\nReturns:\n    A Project instance containing the loaded modules."
+          },
+          "load_module": {
+            "name": "load_module",
+            "kind": "function",
+            "path": "docforge.cli.commands.GriffeLoader.load_module",
+            "signature": "<bound method Alias.signature of Alias('load_module', 'docforge.loaders.griffe_loader.GriffeLoader.load_module')>",
+            "docstring": "Load a single module and convert its introspection data into the docforge models.\n\nArgs:\n    path: The dotted path of the module to load.\n\nReturns:\n    A Module instance."
+          }
+        }
+      },
+      "mkdocs_logic": {
+        "name": "mkdocs_logic",
+        "kind": "module",
+        "path": "docforge.cli.commands.mkdocs_logic",
+        "signature": "<bound method Alias.signature of Alias('mkdocs_logic', 'docforge.cli.mkdocs.logic')>",
+        "docstring": null,
+        "members": {
+          "Path": {
+            "name": "Path",
+            "kind": "alias",
+            "path": "docforge.cli.commands.mkdocs_logic.Path",
+            "signature": "<bound method Alias.signature of Alias('Path', 'docforge.cli.mkdocs.logic.Path')>",
+            "docstring": null
+          },
+          "resources": {
+            "name": "resources",
+            "kind": "alias",
+            "path": "docforge.cli.commands.mkdocs_logic.resources",
+            "signature": "<bound method Alias.signature of Alias('resources', 'docforge.cli.mkdocs.logic.resources')>",
+            "docstring": null
+          },
+          "click": {
+            "name": "click",
+            "kind": "alias",
+            "path": "docforge.cli.commands.mkdocs_logic.click",
+            "signature": "<bound method Alias.signature of Alias('click', 'docforge.cli.mkdocs.logic.click')>",
+            "docstring": null
+          },
+          "yaml": {
+            "name": "yaml",
+            "kind": "alias",
+            "path": "docforge.cli.commands.mkdocs_logic.yaml",
+            "signature": "<bound method Alias.signature of Alias('yaml', 'docforge.cli.mkdocs.logic.yaml')>",
+            "docstring": null
+          },
+          "GriffeLoader": {
+            "name": "GriffeLoader",
+            "kind": "class",
+            "path": "docforge.cli.commands.mkdocs_logic.GriffeLoader",
+            "signature": "<bound method Alias.signature of Alias('GriffeLoader', 'docforge.cli.mkdocs.logic.GriffeLoader')>",
+            "docstring": "Loads Python modules and extracts documentation using the Griffe introspection engine.",
+            "members": {
+              "load_project": {
+                "name": "load_project",
+                "kind": "function",
+                "path": "docforge.cli.commands.mkdocs_logic.GriffeLoader.load_project",
+                "signature": "<bound method Alias.signature of Alias('load_project', 'docforge.loaders.griffe_loader.GriffeLoader.load_project')>",
+                "docstring": "Load multiple modules and combine them into a single Project models.\n\nArgs:\n    module_paths: A list of dotted paths to the modules to load.\n    project_name: Optional name for the project. Defaults to the first module name.\n    skip_import_errors: If True, modules that fail to import will be skipped.\n\nReturns:\n    A Project instance containing the loaded modules."
+              },
+              "load_module": {
+                "name": "load_module",
+                "kind": "function",
+                "path": "docforge.cli.commands.mkdocs_logic.GriffeLoader.load_module",
+                "signature": "<bound method Alias.signature of Alias('load_module', 'docforge.loaders.griffe_loader.GriffeLoader.load_module')>",
+                "docstring": "Load a single module and convert its introspection data into the docforge models.\n\nArgs:\n    path: The dotted path of the module to load.\n\nReturns:\n    A Module instance."
+              }
+            }
+          },
+          "discover_module_paths": {
+            "name": "discover_module_paths",
+            "kind": "function",
+            "path": "docforge.cli.commands.mkdocs_logic.discover_module_paths",
+            "signature": "<bound method Alias.signature of Alias('discover_module_paths', 'docforge.cli.mkdocs.logic.discover_module_paths')>",
+            "docstring": "Discover all Python modules under a package via filesystem traversal.\n\nRules:\n- Directory with __init__.py is treated as a package.\n- Any .py file is treated as a module.\n- All paths are converted to dotted module paths.\n\nArgs:\n    module_name: The name of the package to discover.\n    project_root: The root directory of the project. Defaults to current working directory.\n\nReturns:\n    A sorted list of dotted module paths."
+          },
+          "MkDocsRenderer": {
+            "name": "MkDocsRenderer",
+            "kind": "class",
+            "path": "docforge.cli.commands.mkdocs_logic.MkDocsRenderer",
+            "signature": "<bound method Alias.signature of Alias('MkDocsRenderer', 'docforge.cli.mkdocs.logic.MkDocsRenderer')>",
+            "docstring": "Renderer that generates Markdown source files formatted for the MkDocs\n'mkdocstrings' plugin.",
+            "members": {
+              "name": {
+                "name": "name",
+                "kind": "attribute",
+                "path": "docforge.cli.commands.mkdocs_logic.MkDocsRenderer.name",
+                "signature": "<bound method Alias.signature of Alias('name', 'docforge.renderers.mkdocs_renderer.MkDocsRenderer.name')>",
+                "docstring": null
+              },
+              "generate_sources": {
+                "name": "generate_sources",
+                "kind": "function",
+                "path": "docforge.cli.commands.mkdocs_logic.MkDocsRenderer.generate_sources",
+                "signature": "<bound method Alias.signature of Alias('generate_sources', 'docforge.renderers.mkdocs_renderer.MkDocsRenderer.generate_sources')>",
+                "docstring": "Produce a set of Markdown files in the output directory based on the\nprovided Project models.\n\nArgs:\n    project: The project models to render.\n    out_dir: Target directory for documentation files."
+              }
+            }
+          },
+          "load_nav_spec": {
+            "name": "load_nav_spec",
+            "kind": "function",
+            "path": "docforge.cli.commands.mkdocs_logic.load_nav_spec",
+            "signature": "<bound method Alias.signature of Alias('load_nav_spec', 'docforge.cli.mkdocs.logic.load_nav_spec')>",
+            "docstring": "Utility function to load a NavSpec from a file.\n\nArgs:\n    path: Path to the navigation specification file.\n\nReturns:\n    A loaded NavSpec instance."
+          },
+          "resolve_nav": {
+            "name": "resolve_nav",
+            "kind": "function",
+            "path": "docforge.cli.commands.mkdocs_logic.resolve_nav",
+            "signature": "<bound method Alias.signature of Alias('resolve_nav', 'docforge.cli.mkdocs.logic.resolve_nav')>",
+            "docstring": "Create a ResolvedNav by processing a NavSpec against the filesystem.\nThis expands globs and validates the existence of referenced files.\n\nArgs:\n    spec: The navigation specification to resolve.\n    docs_root: The root directory for documentation files.\n\nReturns:\n    A ResolvedNav instance.\n\nRaises:\n    FileNotFoundError: If a pattern doesn't match any files or the docs_root doesn't exist."
+          },
+          "MkDocsNavEmitter": {
+            "name": "MkDocsNavEmitter",
+            "kind": "class",
+            "path": "docforge.cli.commands.mkdocs_logic.MkDocsNavEmitter",
+            "signature": "<bound method Alias.signature of Alias('MkDocsNavEmitter', 'docforge.cli.mkdocs.logic.MkDocsNavEmitter')>",
+            "docstring": "Emitter responsible for transforming a ResolvedNav into an MkDocs-compatible\nnavigation structure.",
+            "members": {
+              "emit": {
+                "name": "emit",
+                "kind": "function",
+                "path": "docforge.cli.commands.mkdocs_logic.MkDocsNavEmitter.emit",
+                "signature": "<bound method Alias.signature of Alias('emit', 'docforge.nav.mkdocs.MkDocsNavEmitter.emit')>",
+                "docstring": "Generate a list of navigation entries for mkdocs.yml.\n\nArgs:\n    nav: The resolved navigation data.\n\nReturns:\n    A list of dictionary mappings representing the MkDocs navigation."
+              }
+            }
+          },
+          "generate_sources": {
+            "name": "generate_sources",
+            "kind": "function",
+            "path": "docforge.cli.commands.mkdocs_logic.generate_sources",
+            "signature": "<bound method Alias.signature of Alias('generate_sources', 'docforge.cli.mkdocs.logic.generate_sources')>",
+            "docstring": "Generate Markdown source files for the specified module."
+          },
+          "generate_config": {
+            "name": "generate_config",
+            "kind": "function",
+            "path": "docforge.cli.commands.mkdocs_logic.generate_config",
+            "signature": "<bound method Alias.signature of Alias('generate_config', 'docforge.cli.mkdocs.logic.generate_config')>",
+            "docstring": "Generate an mkdocs.yml configuration file."
+          },
+          "build": {
+            "name": "build",
+            "kind": "function",
+            "path": "docforge.cli.commands.mkdocs_logic.build",
+            "signature": "<bound method Alias.signature of Alias('build', 'docforge.cli.mkdocs.logic.build')>",
+            "docstring": "Build the documentation site using MkDocs."
+          },
+          "serve": {
+            "name": "serve",
+            "kind": "function",
+            "path": "docforge.cli.commands.mkdocs_logic.serve",
+            "signature": "<bound method Alias.signature of Alias('serve', 'docforge.cli.mkdocs.logic.serve')>",
+            "docstring": "Serve the documentation site with live-reload using MkDocs."
+          }
+        }
+      },
+      "mcp_logic": {
+        "name": "mcp_logic",
+        "kind": "module",
+        "path": "docforge.cli.commands.mcp_logic",
+        "signature": "<bound method Alias.signature of Alias('mcp_logic', 'docforge.cli.mcp.logic')>",
+        "docstring": null,
+        "members": {
+          "Path": {
+            "name": "Path",
+            "kind": "alias",
+            "path": "docforge.cli.commands.mcp_logic.Path",
+            "signature": "<bound method Alias.signature of Alias('Path', 'docforge.cli.mcp.logic.Path')>",
+            "docstring": null
+          },
+          "click": {
+            "name": "click",
+            "kind": "alias",
+            "path": "docforge.cli.commands.mcp_logic.click",
+            "signature": "<bound method Alias.signature of Alias('click', 'docforge.cli.mcp.logic.click')>",
+            "docstring": null
+          },
+          "GriffeLoader": {
+            "name": "GriffeLoader",
+            "kind": "class",
+            "path": "docforge.cli.commands.mcp_logic.GriffeLoader",
+            "signature": "<bound method Alias.signature of Alias('GriffeLoader', 'docforge.cli.mcp.logic.GriffeLoader')>",
+            "docstring": "Loads Python modules and extracts documentation using the Griffe introspection engine.",
+            "members": {
+              "load_project": {
+                "name": "load_project",
+                "kind": "function",
+                "path": "docforge.cli.commands.mcp_logic.GriffeLoader.load_project",
+                "signature": "<bound method Alias.signature of Alias('load_project', 'docforge.loaders.griffe_loader.GriffeLoader.load_project')>",
+                "docstring": "Load multiple modules and combine them into a single Project models.\n\nArgs:\n    module_paths: A list of dotted paths to the modules to load.\n    project_name: Optional name for the project. Defaults to the first module name.\n    skip_import_errors: If True, modules that fail to import will be skipped.\n\nReturns:\n    A Project instance containing the loaded modules."
+              },
+              "load_module": {
+                "name": "load_module",
+                "kind": "function",
+                "path": "docforge.cli.commands.mcp_logic.GriffeLoader.load_module",
+                "signature": "<bound method Alias.signature of Alias('load_module', 'docforge.loaders.griffe_loader.GriffeLoader.load_module')>",
+                "docstring": "Load a single module and convert its introspection data into the docforge models.\n\nArgs:\n    path: The dotted path of the module to load.\n\nReturns:\n    A Module instance."
+              }
+            }
+          },
+          "discover_module_paths": {
+            "name": "discover_module_paths",
+            "kind": "function",
+            "path": "docforge.cli.commands.mcp_logic.discover_module_paths",
+            "signature": "<bound method Alias.signature of Alias('discover_module_paths', 'docforge.cli.mcp.logic.discover_module_paths')>",
+            "docstring": "Discover all Python modules under a package via filesystem traversal.\n\nRules:\n- Directory with __init__.py is treated as a package.\n- Any .py file is treated as a module.\n- All paths are converted to dotted module paths.\n\nArgs:\n    module_name: The name of the package to discover.\n    project_root: The root directory of the project. Defaults to current working directory.\n\nReturns:\n    A sorted list of dotted module paths."
+          },
+          "MCPRenderer": {
+            "name": "MCPRenderer",
+            "kind": "class",
+            "path": "docforge.cli.commands.mcp_logic.MCPRenderer",
+            "signature": "<bound method Alias.signature of Alias('MCPRenderer', 'docforge.cli.mcp.logic.MCPRenderer')>",
+            "docstring": "Renderer that emits MCP-native JSON resources from docforge models.",
+            "members": {
+              "name": {
+                "name": "name",
+                "kind": "attribute",
+                "path": "docforge.cli.commands.mcp_logic.MCPRenderer.name",
+                "signature": "<bound method Alias.signature of Alias('name', 'docforge.renderers.mcp_renderer.MCPRenderer.name')>",
+                "docstring": null
+              },
+              "generate_sources": {
+                "name": "generate_sources",
+                "kind": "function",
+                "path": "docforge.cli.commands.mcp_logic.MCPRenderer.generate_sources",
+                "signature": "<bound method Alias.signature of Alias('generate_sources', 'docforge.renderers.mcp_renderer.MCPRenderer.generate_sources')>",
+                "docstring": "Generate MCP-compatible JSON resources and navigation for the project."
+              }
+            }
+          },
+          "MCPServer": {
+            "name": "MCPServer",
+            "kind": "class",
+            "path": "docforge.cli.commands.mcp_logic.MCPServer",
+            "signature": "<bound method Alias.signature of Alias('MCPServer', 'docforge.cli.mcp.logic.MCPServer')>",
+            "docstring": "MCP server for serving a pre-built MCP documentation bundle.",
+            "members": {
+              "mcp_root": {
+                "name": "mcp_root",
+                "kind": "attribute",
+                "path": "docforge.cli.commands.mcp_logic.MCPServer.mcp_root",
+                "signature": "<bound method Alias.signature of Alias('mcp_root', 'docforge.servers.mcp_server.MCPServer.mcp_root')>",
+                "docstring": null
+              },
+              "app": {
+                "name": "app",
+                "kind": "attribute",
+                "path": "docforge.cli.commands.mcp_logic.MCPServer.app",
+                "signature": "<bound method Alias.signature of Alias('app', 'docforge.servers.mcp_server.MCPServer.app')>",
+                "docstring": null
+              },
+              "run": {
+                "name": "run",
+                "kind": "function",
+                "path": "docforge.cli.commands.mcp_logic.MCPServer.run",
+                "signature": "<bound method Alias.signature of Alias('run', 'docforge.servers.mcp_server.MCPServer.run')>",
+                "docstring": "Start the MCP server.\n\nArgs:\n    transport: MCP transport (default: streamable-http)"
+              }
+            }
+          },
+          "generate_resources": {
+            "name": "generate_resources",
+            "kind": "function",
+            "path": "docforge.cli.commands.mcp_logic.generate_resources",
+            "signature": "<bound method Alias.signature of Alias('generate_resources', 'docforge.cli.mcp.logic.generate_resources')>",
+            "docstring": "Generate MCP-compatible documentation resources."
+          },
+          "serve": {
+            "name": "serve",
+            "kind": "function",
+            "path": "docforge.cli.commands.mcp_logic.serve",
+            "signature": "<bound method Alias.signature of Alias('serve', 'docforge.cli.mcp.logic.serve')>",
+            "docstring": "Serve MCP documentation."
+          }
+        }
+      },
+      "cli": {
+        "name": "cli",
+        "kind": "function",
+        "path": "docforge.cli.commands.cli",
+        "signature": "<bound method Function.signature of Function('cli', 8, 14)>",
+        "docstring": "doc-forge CLI: A tool for introspecting Python projects and generating\ndocumentation."
+      },
+      "build": {
+        "name": "build",
+        "kind": "function",
+        "path": "docforge.cli.commands.build",
+        "signature": "<bound method Function.signature of Function('build', 16, 69)>",
+        "docstring": "Build documentation (MkDocs site or MCP resources)."
+      },
+      "serve": {
+        "name": "serve",
+        "kind": "function",
+        "path": "docforge.cli.commands.serve",
+        "signature": "<bound method Function.signature of Function('serve', 71, 93)>",
+        "docstring": "Serve documentation."
+      },
+      "tree": {
+        "name": "tree",
+        "kind": "function",
+        "path": "docforge.cli.commands.tree",
+        "signature": "<bound method Function.signature of Function('tree', 95, 121)>",
+        "docstring": "Visualize the project structure."
+      }
+    }
+  }
+}

mcp_docs/modules/docforge.cli.json

@@ -9,54 +9,135 @@
         "kind": "module",
         "path": "docforge.cli.main",
         "signature": null,
-        "docstring": "Main entry point for the doc-forge CLI. This module defines the core command\ngroup and the 'tree', 'generate', 'build', and 'serve' commands.",
+        "docstring": "Main entry point for the doc-forge CLI.",
         "members": {
+          "cli": {
+            "name": "cli",
+            "kind": "function",
+            "path": "docforge.cli.main.cli",
+            "signature": "<bound method Alias.signature of Alias('cli', 'docforge.cli.commands.cli')>",
+            "docstring": "doc-forge CLI: A tool for introspecting Python projects and generating\ndocumentation."
+          },
+          "main": {
+            "name": "main",
+            "kind": "function",
+            "path": "docforge.cli.main.main",
+            "signature": "<bound method Function.signature of Function('main', 6, 10)>",
+            "docstring": "CLI Entry point. Boots the click application."
+          }
+        }
+      },
+      "commands": {
+        "name": "commands",
+        "kind": "module",
+        "path": "docforge.cli.commands",
+        "signature": null,
+        "docstring": null,
+        "members": {
+          "click": {
+            "name": "click",
+            "kind": "alias",
+            "path": "docforge.cli.commands.click",
+            "signature": "<bound method Alias.signature of Alias('click', 'click')>",
+            "docstring": null
+          },
           "Path": {
             "name": "Path",
             "kind": "alias",
-            "path": "docforge.cli.main.Path",
+            "path": "docforge.cli.commands.Path",
             "signature": "<bound method Alias.signature of Alias('Path', 'pathlib.Path')>",
             "docstring": null
           },
           "Sequence": {
             "name": "Sequence",
             "kind": "alias",
-            "path": "docforge.cli.main.Sequence",
+            "path": "docforge.cli.commands.Sequence",
             "signature": "<bound method Alias.signature of Alias('Sequence', 'typing.Sequence')>",
             "docstring": null
           },
           "Optional": {
             "name": "Optional",
             "kind": "alias",
-            "path": "docforge.cli.main.Optional",
+            "path": "docforge.cli.commands.Optional",
             "signature": "<bound method Alias.signature of Alias('Optional', 'typing.Optional')>",
             "docstring": null
           },
-          "click": {
-            "name": "click",
-            "kind": "alias",
-            "path": "docforge.cli.main.click",
-            "signature": "<bound method Alias.signature of Alias('click', 'click')>",
-            "docstring": null
-          },
           "GriffeLoader": {
             "name": "GriffeLoader",
             "kind": "class",
-            "path": "docforge.cli.main.GriffeLoader",
+            "path": "docforge.cli.commands.GriffeLoader",
             "signature": "<bound method Alias.signature of Alias('GriffeLoader', 'docforge.loaders.GriffeLoader')>",
             "docstring": "Loads Python modules and extracts documentation using the Griffe introspection engine.",
             "members": {
               "load_project": {
                 "name": "load_project",
                 "kind": "function",
-                "path": "docforge.cli.main.GriffeLoader.load_project",
+                "path": "docforge.cli.commands.GriffeLoader.load_project",
                 "signature": "<bound method Alias.signature of Alias('load_project', 'docforge.loaders.griffe_loader.GriffeLoader.load_project')>",
                 "docstring": "Load multiple modules and combine them into a single Project models.\n\nArgs:\n    module_paths: A list of dotted paths to the modules to load.\n    project_name: Optional name for the project. Defaults to the first module name.\n    skip_import_errors: If True, modules that fail to import will be skipped.\n\nReturns:\n    A Project instance containing the loaded modules."
               },
               "load_module": {
                 "name": "load_module",
                 "kind": "function",
-                "path": "docforge.cli.main.GriffeLoader.load_module",
+                "path": "docforge.cli.commands.GriffeLoader.load_module",
+                "signature": "<bound method Alias.signature of Alias('load_module', 'docforge.loaders.griffe_loader.GriffeLoader.load_module')>",
+                "docstring": "Load a single module and convert its introspection data into the docforge models.\n\nArgs:\n    path: The dotted path of the module to load.\n\nReturns:\n    A Module instance."
+              }
+            }
+          },
+          "mkdocs_logic": {
+            "name": "mkdocs_logic",
+            "kind": "module",
+            "path": "docforge.cli.commands.mkdocs_logic",
+            "signature": "<bound method Alias.signature of Alias('mkdocs_logic', 'docforge.cli.mkdocs.logic')>",
+            "docstring": null,
+            "members": {
+              "Path": {
+                "name": "Path",
+                "kind": "alias",
+                "path": "docforge.cli.commands.mkdocs_logic.Path",
+                "signature": "<bound method Alias.signature of Alias('Path', 'docforge.cli.mkdocs.logic.Path')>",
+                "docstring": null
+              },
+              "resources": {
+                "name": "resources",
+                "kind": "alias",
+                "path": "docforge.cli.commands.mkdocs_logic.resources",
+                "signature": "<bound method Alias.signature of Alias('resources', 'docforge.cli.mkdocs.logic.resources')>",
+                "docstring": null
+              },
+              "click": {
+                "name": "click",
+                "kind": "alias",
+                "path": "docforge.cli.commands.mkdocs_logic.click",
+                "signature": "<bound method Alias.signature of Alias('click', 'docforge.cli.mkdocs.logic.click')>",
+                "docstring": null
+              },
+              "yaml": {
+                "name": "yaml",
+                "kind": "alias",
+                "path": "docforge.cli.commands.mkdocs_logic.yaml",
+                "signature": "<bound method Alias.signature of Alias('yaml', 'docforge.cli.mkdocs.logic.yaml')>",
+                "docstring": null
+              },
+              "GriffeLoader": {
+                "name": "GriffeLoader",
+                "kind": "class",
+                "path": "docforge.cli.commands.mkdocs_logic.GriffeLoader",
+                "signature": "<bound method Alias.signature of Alias('GriffeLoader', 'docforge.cli.mkdocs.logic.GriffeLoader')>",
+                "docstring": "Loads Python modules and extracts documentation using the Griffe introspection engine.",
+                "members": {
+                  "load_project": {
+                    "name": "load_project",
+                    "kind": "function",
+                    "path": "docforge.cli.commands.mkdocs_logic.GriffeLoader.load_project",
+                    "signature": "<bound method Alias.signature of Alias('load_project', 'docforge.loaders.griffe_loader.GriffeLoader.load_project')>",
+                    "docstring": "Load multiple modules and combine them into a single Project models.\n\nArgs:\n    module_paths: A list of dotted paths to the modules to load.\n    project_name: Optional name for the project. Defaults to the first module name.\n    skip_import_errors: If True, modules that fail to import will be skipped.\n\nReturns:\n    A Project instance containing the loaded modules."
+                  },
+                  "load_module": {
+                    "name": "load_module",
+                    "kind": "function",
+                    "path": "docforge.cli.commands.mkdocs_logic.GriffeLoader.load_module",
                     "signature": "<bound method Alias.signature of Alias('load_module', 'docforge.loaders.griffe_loader.GriffeLoader.load_module')>",
                     "docstring": "Load a single module and convert its introspection data into the docforge models.\n\nArgs:\n    path: The dotted path of the module to load.\n\nReturns:\n    A Module instance."
                   }
@@ -65,118 +146,369 @@
               "discover_module_paths": {
                 "name": "discover_module_paths",
                 "kind": "function",
-            "path": "docforge.cli.main.discover_module_paths",
-            "signature": "<bound method Alias.signature of Alias('discover_module_paths', 'docforge.loaders.discover_module_paths')>",
+                "path": "docforge.cli.commands.mkdocs_logic.discover_module_paths",
+                "signature": "<bound method Alias.signature of Alias('discover_module_paths', 'docforge.cli.mkdocs.logic.discover_module_paths')>",
                 "docstring": "Discover all Python modules under a package via filesystem traversal.\n\nRules:\n- Directory with __init__.py is treated as a package.\n- Any .py file is treated as a module.\n- All paths are converted to dotted module paths.\n\nArgs:\n    module_name: The name of the package to discover.\n    project_root: The root directory of the project. Defaults to current working directory.\n\nReturns:\n    A sorted list of dotted module paths."
               },
               "MkDocsRenderer": {
                 "name": "MkDocsRenderer",
                 "kind": "class",
-            "path": "docforge.cli.main.MkDocsRenderer",
-            "signature": "<bound method Alias.signature of Alias('MkDocsRenderer', 'docforge.renderers.MkDocsRenderer')>",
+                "path": "docforge.cli.commands.mkdocs_logic.MkDocsRenderer",
+                "signature": "<bound method Alias.signature of Alias('MkDocsRenderer', 'docforge.cli.mkdocs.logic.MkDocsRenderer')>",
                 "docstring": "Renderer that generates Markdown source files formatted for the MkDocs\n'mkdocstrings' plugin.",
                 "members": {
                   "name": {
                     "name": "name",
                     "kind": "attribute",
-                "path": "docforge.cli.main.MkDocsRenderer.name",
+                    "path": "docforge.cli.commands.mkdocs_logic.MkDocsRenderer.name",
                     "signature": "<bound method Alias.signature of Alias('name', 'docforge.renderers.mkdocs_renderer.MkDocsRenderer.name')>",
                     "docstring": null
                   },
                   "generate_sources": {
                     "name": "generate_sources",
                     "kind": "function",
-                "path": "docforge.cli.main.MkDocsRenderer.generate_sources",
+                    "path": "docforge.cli.commands.mkdocs_logic.MkDocsRenderer.generate_sources",
                     "signature": "<bound method Alias.signature of Alias('generate_sources', 'docforge.renderers.mkdocs_renderer.MkDocsRenderer.generate_sources')>",
                     "docstring": "Produce a set of Markdown files in the output directory based on the\nprovided Project models.\n\nArgs:\n    project: The project models to render.\n    out_dir: Target directory for documentation files."
                   }
                 }
               },
+              "load_nav_spec": {
+                "name": "load_nav_spec",
+                "kind": "function",
+                "path": "docforge.cli.commands.mkdocs_logic.load_nav_spec",
+                "signature": "<bound method Alias.signature of Alias('load_nav_spec', 'docforge.cli.mkdocs.logic.load_nav_spec')>",
+                "docstring": "Utility function to load a NavSpec from a file.\n\nArgs:\n    path: Path to the navigation specification file.\n\nReturns:\n    A loaded NavSpec instance."
+              },
+              "resolve_nav": {
+                "name": "resolve_nav",
+                "kind": "function",
+                "path": "docforge.cli.commands.mkdocs_logic.resolve_nav",
+                "signature": "<bound method Alias.signature of Alias('resolve_nav', 'docforge.cli.mkdocs.logic.resolve_nav')>",
+                "docstring": "Create a ResolvedNav by processing a NavSpec against the filesystem.\nThis expands globs and validates the existence of referenced files.\n\nArgs:\n    spec: The navigation specification to resolve.\n    docs_root: The root directory for documentation files.\n\nReturns:\n    A ResolvedNav instance.\n\nRaises:\n    FileNotFoundError: If a pattern doesn't match any files or the docs_root doesn't exist."
+              },
+              "MkDocsNavEmitter": {
+                "name": "MkDocsNavEmitter",
+                "kind": "class",
+                "path": "docforge.cli.commands.mkdocs_logic.MkDocsNavEmitter",
+                "signature": "<bound method Alias.signature of Alias('MkDocsNavEmitter', 'docforge.cli.mkdocs.logic.MkDocsNavEmitter')>",
+                "docstring": "Emitter responsible for transforming a ResolvedNav into an MkDocs-compatible\nnavigation structure.",
+                "members": {
+                  "emit": {
+                    "name": "emit",
+                    "kind": "function",
+                    "path": "docforge.cli.commands.mkdocs_logic.MkDocsNavEmitter.emit",
+                    "signature": "<bound method Alias.signature of Alias('emit', 'docforge.nav.mkdocs.MkDocsNavEmitter.emit')>",
+                    "docstring": "Generate a list of navigation entries for mkdocs.yml.\n\nArgs:\n    nav: The resolved navigation data.\n\nReturns:\n    A list of dictionary mappings representing the MkDocs navigation."
+                  }
+                }
+              },
+              "generate_sources": {
+                "name": "generate_sources",
+                "kind": "function",
+                "path": "docforge.cli.commands.mkdocs_logic.generate_sources",
+                "signature": "<bound method Alias.signature of Alias('generate_sources', 'docforge.cli.mkdocs.logic.generate_sources')>",
+                "docstring": "Generate Markdown source files for the specified module."
+              },
+              "generate_config": {
+                "name": "generate_config",
+                "kind": "function",
+                "path": "docforge.cli.commands.mkdocs_logic.generate_config",
+                "signature": "<bound method Alias.signature of Alias('generate_config', 'docforge.cli.mkdocs.logic.generate_config')>",
+                "docstring": "Generate an mkdocs.yml configuration file."
+              },
+              "build": {
+                "name": "build",
+                "kind": "function",
+                "path": "docforge.cli.commands.mkdocs_logic.build",
+                "signature": "<bound method Alias.signature of Alias('build', 'docforge.cli.mkdocs.logic.build')>",
+                "docstring": "Build the documentation site using MkDocs."
+              },
+              "serve": {
+                "name": "serve",
+                "kind": "function",
+                "path": "docforge.cli.commands.mkdocs_logic.serve",
+                "signature": "<bound method Alias.signature of Alias('serve', 'docforge.cli.mkdocs.logic.serve')>",
+                "docstring": "Serve the documentation site with live-reload using MkDocs."
+              }
+            }
+          },
+          "mcp_logic": {
+            "name": "mcp_logic",
+            "kind": "module",
+            "path": "docforge.cli.commands.mcp_logic",
+            "signature": "<bound method Alias.signature of Alias('mcp_logic', 'docforge.cli.mcp.logic')>",
+            "docstring": null,
+            "members": {
+              "Path": {
+                "name": "Path",
+                "kind": "alias",
+                "path": "docforge.cli.commands.mcp_logic.Path",
+                "signature": "<bound method Alias.signature of Alias('Path', 'docforge.cli.mcp.logic.Path')>",
+                "docstring": null
+              },
+              "click": {
+                "name": "click",
+                "kind": "alias",
+                "path": "docforge.cli.commands.mcp_logic.click",
+                "signature": "<bound method Alias.signature of Alias('click', 'docforge.cli.mcp.logic.click')>",
+                "docstring": null
+              },
+              "GriffeLoader": {
+                "name": "GriffeLoader",
+                "kind": "class",
+                "path": "docforge.cli.commands.mcp_logic.GriffeLoader",
+                "signature": "<bound method Alias.signature of Alias('GriffeLoader', 'docforge.cli.mcp.logic.GriffeLoader')>",
+                "docstring": "Loads Python modules and extracts documentation using the Griffe introspection engine.",
+                "members": {
+                  "load_project": {
+                    "name": "load_project",
+                    "kind": "function",
+                    "path": "docforge.cli.commands.mcp_logic.GriffeLoader.load_project",
+                    "signature": "<bound method Alias.signature of Alias('load_project', 'docforge.loaders.griffe_loader.GriffeLoader.load_project')>",
+                    "docstring": "Load multiple modules and combine them into a single Project models.\n\nArgs:\n    module_paths: A list of dotted paths to the modules to load.\n    project_name: Optional name for the project. Defaults to the first module name.\n    skip_import_errors: If True, modules that fail to import will be skipped.\n\nReturns:\n    A Project instance containing the loaded modules."
+                  },
+                  "load_module": {
+                    "name": "load_module",
+                    "kind": "function",
+                    "path": "docforge.cli.commands.mcp_logic.GriffeLoader.load_module",
+                    "signature": "<bound method Alias.signature of Alias('load_module', 'docforge.loaders.griffe_loader.GriffeLoader.load_module')>",
+                    "docstring": "Load a single module and convert its introspection data into the docforge models.\n\nArgs:\n    path: The dotted path of the module to load.\n\nReturns:\n    A Module instance."
+                  }
+                }
+              },
+              "discover_module_paths": {
+                "name": "discover_module_paths",
+                "kind": "function",
+                "path": "docforge.cli.commands.mcp_logic.discover_module_paths",
+                "signature": "<bound method Alias.signature of Alias('discover_module_paths', 'docforge.cli.mcp.logic.discover_module_paths')>",
+                "docstring": "Discover all Python modules under a package via filesystem traversal.\n\nRules:\n- Directory with __init__.py is treated as a package.\n- Any .py file is treated as a module.\n- All paths are converted to dotted module paths.\n\nArgs:\n    module_name: The name of the package to discover.\n    project_root: The root directory of the project. Defaults to current working directory.\n\nReturns:\n    A sorted list of dotted module paths."
+              },
               "MCPRenderer": {
                 "name": "MCPRenderer",
                 "kind": "class",
-            "path": "docforge.cli.main.MCPRenderer",
-            "signature": "<bound method Alias.signature of Alias('MCPRenderer', 'docforge.renderers.MCPRenderer')>",
+                "path": "docforge.cli.commands.mcp_logic.MCPRenderer",
+                "signature": "<bound method Alias.signature of Alias('MCPRenderer', 'docforge.cli.mcp.logic.MCPRenderer')>",
                 "docstring": "Renderer that emits MCP-native JSON resources from docforge models.",
                 "members": {
                   "name": {
                     "name": "name",
                     "kind": "attribute",
-                "path": "docforge.cli.main.MCPRenderer.name",
+                    "path": "docforge.cli.commands.mcp_logic.MCPRenderer.name",
                     "signature": "<bound method Alias.signature of Alias('name', 'docforge.renderers.mcp_renderer.MCPRenderer.name')>",
                     "docstring": null
                   },
                   "generate_sources": {
                     "name": "generate_sources",
                     "kind": "function",
-                "path": "docforge.cli.main.MCPRenderer.generate_sources",
+                    "path": "docforge.cli.commands.mcp_logic.MCPRenderer.generate_sources",
                     "signature": "<bound method Alias.signature of Alias('generate_sources', 'docforge.renderers.mcp_renderer.MCPRenderer.generate_sources')>",
                     "docstring": "Generate MCP-compatible JSON resources and navigation for the project."
                   }
                 }
               },
-          "mkdocs_cmd": {
-            "name": "mkdocs_cmd",
-            "kind": "function",
-            "path": "docforge.cli.main.mkdocs_cmd",
-            "signature": "<bound method Alias.signature of Alias('mkdocs_cmd', 'docforge.cli.mkdocs.mkdocs_cmd')>",
-            "docstring": "Generate an mkdocs.yml configuration file by combining a template with\nthe navigation structure resolved from a docforge.nav.yml file.\n\nArgs:\n    docs_dir: Path to the directory containing documentation Markdown files.\n    nav_file: Path to the docforge.nav.yml specification.\n    template: Optional path to an mkdocs.yml template.\n    out: Path where the final mkdocs.yml will be written.\n    site_name: The name of the documentation site."
+              "MCPServer": {
+                "name": "MCPServer",
+                "kind": "class",
+                "path": "docforge.cli.commands.mcp_logic.MCPServer",
+                "signature": "<bound method Alias.signature of Alias('MCPServer', 'docforge.cli.mcp.logic.MCPServer')>",
+                "docstring": "MCP server for serving a pre-built MCP documentation bundle.",
+                "members": {
+                  "mcp_root": {
+                    "name": "mcp_root",
+                    "kind": "attribute",
+                    "path": "docforge.cli.commands.mcp_logic.MCPServer.mcp_root",
+                    "signature": "<bound method Alias.signature of Alias('mcp_root', 'docforge.servers.mcp_server.MCPServer.mcp_root')>",
+                    "docstring": null
                   },
-          "cli": {
-            "name": "cli",
-            "kind": "function",
-            "path": "docforge.cli.main.cli",
-            "signature": "<bound method Function.signature of Function('cli', 16, 22)>",
-            "docstring": "doc-forge CLI: A tool for introspecting Python projects and generating\ndocumentation."
+                  "app": {
+                    "name": "app",
+                    "kind": "attribute",
+                    "path": "docforge.cli.commands.mcp_logic.MCPServer.app",
+                    "signature": "<bound method Alias.signature of Alias('app', 'docforge.servers.mcp_server.MCPServer.app')>",
+                    "docstring": null
                   },
-          "tree": {
-            "name": "tree",
+                  "run": {
+                    "name": "run",
                     "kind": "function",
-            "path": "docforge.cli.main.tree",
-            "signature": "<bound method Function.signature of Function('tree', 31, 62)>",
-            "docstring": "Visualize the project structure including modules and their members.\n\nArgs:\n    modules: List of module paths to introspect.\n    project_name: Optional project name override."
+                    "path": "docforge.cli.commands.mcp_logic.MCPServer.run",
+                    "signature": "<bound method Alias.signature of Alias('run', 'docforge.servers.mcp_server.MCPServer.run')>",
+                    "docstring": "Start the MCP server.\n\nArgs:\n    transport: MCP transport (default: streamable-http)"
+                  }
+                }
               },
-          "generate": {
-            "name": "generate",
+              "generate_resources": {
+                "name": "generate_resources",
                 "kind": "function",
-            "path": "docforge.cli.main.generate",
-            "signature": "<bound method Function.signature of Function('generate', 82, 122)>",
-            "docstring": "Generate Markdown source files for the specified module.\n\nArgs:\n    module: The primary module path to document.\n    project_name: Optional project name override.\n    docs_dir: Directory where documentation sources will be written."
-          },
-          "generate_mcp": {
-            "name": "generate_mcp",
-            "kind": "function",
-            "path": "docforge.cli.main.generate_mcp",
-            "signature": "<bound method Function.signature of Function('generate_mcp', 129, 168)>",
-            "docstring": "Generate MCP-compatible documentation resources for the specified module.\n\nArgs:\n    module: The primary module path to document.\n    project_name: Optional project name override.\n    out_dir: Directory where MCP resources will be written."
-          },
-          "build": {
-            "name": "build",
-            "kind": "function",
-            "path": "docforge.cli.main.build",
-            "signature": "<bound method Function.signature of Function('build', 175, 196)>",
-            "docstring": "Build the documentation site using MkDocs.\n\nArgs:\n    mkdocs_yml: Path to the mkdocs.yml configuration file."
-          },
-          "serve_mcp": {
-            "name": "serve_mcp",
-            "kind": "function",
-            "path": "docforge.cli.main.serve_mcp",
-            "signature": "<bound method Function.signature of Function('serve_mcp', 203, 230)>",
-            "docstring": "Serve MCP documentation from the local mcp_docs directory."
+                "path": "docforge.cli.commands.mcp_logic.generate_resources",
+                "signature": "<bound method Alias.signature of Alias('generate_resources', 'docforge.cli.mcp.logic.generate_resources')>",
+                "docstring": "Generate MCP-compatible documentation resources."
               },
               "serve": {
                 "name": "serve",
                 "kind": "function",
-            "path": "docforge.cli.main.serve",
-            "signature": "<bound method Function.signature of Function('serve', 237, 260)>",
-            "docstring": "Serve the documentation site with live-reload using MkDocs.\n\nArgs:\n    mkdocs_yml: Path to the mkdocs.yml configuration file."
+                "path": "docforge.cli.commands.mcp_logic.serve",
+                "signature": "<bound method Alias.signature of Alias('serve', 'docforge.cli.mcp.logic.serve')>",
+                "docstring": "Serve MCP documentation."
+              }
+            }
           },
-          "main": {
-            "name": "main",
+          "cli": {
+            "name": "cli",
             "kind": "function",
-            "path": "docforge.cli.main.main",
-            "signature": "<bound method Function.signature of Function('main', 267, 271)>",
-            "docstring": "CLI Entry point. Boots the click application."
+            "path": "docforge.cli.commands.cli",
+            "signature": "<bound method Function.signature of Function('cli', 8, 14)>",
+            "docstring": "doc-forge CLI: A tool for introspecting Python projects and generating\ndocumentation."
+          },
+          "build": {
+            "name": "build",
+            "kind": "function",
+            "path": "docforge.cli.commands.build",
+            "signature": "<bound method Function.signature of Function('build', 16, 69)>",
+            "docstring": "Build documentation (MkDocs site or MCP resources)."
+          },
+          "serve": {
+            "name": "serve",
+            "kind": "function",
+            "path": "docforge.cli.commands.serve",
+            "signature": "<bound method Function.signature of Function('serve', 71, 93)>",
+            "docstring": "Serve documentation."
+          },
+          "tree": {
+            "name": "tree",
+            "kind": "function",
+            "path": "docforge.cli.commands.tree",
+            "signature": "<bound method Function.signature of Function('tree', 95, 121)>",
+            "docstring": "Visualize the project structure."
+          }
+        }
+      },
+      "mcp": {
+        "name": "mcp",
+        "kind": "module",
+        "path": "docforge.cli.mcp",
+        "signature": null,
+        "docstring": null,
+        "members": {
+          "logic": {
+            "name": "logic",
+            "kind": "module",
+            "path": "docforge.cli.mcp.logic",
+            "signature": null,
+            "docstring": null,
+            "members": {
+              "Path": {
+                "name": "Path",
+                "kind": "alias",
+                "path": "docforge.cli.mcp.logic.Path",
+                "signature": "<bound method Alias.signature of Alias('Path', 'pathlib.Path')>",
+                "docstring": null
+              },
+              "click": {
+                "name": "click",
+                "kind": "alias",
+                "path": "docforge.cli.mcp.logic.click",
+                "signature": "<bound method Alias.signature of Alias('click', 'click')>",
+                "docstring": null
+              },
+              "GriffeLoader": {
+                "name": "GriffeLoader",
+                "kind": "class",
+                "path": "docforge.cli.mcp.logic.GriffeLoader",
+                "signature": "<bound method Alias.signature of Alias('GriffeLoader', 'docforge.loaders.GriffeLoader')>",
+                "docstring": "Loads Python modules and extracts documentation using the Griffe introspection engine.",
+                "members": {
+                  "load_project": {
+                    "name": "load_project",
+                    "kind": "function",
+                    "path": "docforge.cli.mcp.logic.GriffeLoader.load_project",
+                    "signature": "<bound method Alias.signature of Alias('load_project', 'docforge.loaders.griffe_loader.GriffeLoader.load_project')>",
+                    "docstring": "Load multiple modules and combine them into a single Project models.\n\nArgs:\n    module_paths: A list of dotted paths to the modules to load.\n    project_name: Optional name for the project. Defaults to the first module name.\n    skip_import_errors: If True, modules that fail to import will be skipped.\n\nReturns:\n    A Project instance containing the loaded modules."
+                  },
+                  "load_module": {
+                    "name": "load_module",
+                    "kind": "function",
+                    "path": "docforge.cli.mcp.logic.GriffeLoader.load_module",
+                    "signature": "<bound method Alias.signature of Alias('load_module', 'docforge.loaders.griffe_loader.GriffeLoader.load_module')>",
+                    "docstring": "Load a single module and convert its introspection data into the docforge models.\n\nArgs:\n    path: The dotted path of the module to load.\n\nReturns:\n    A Module instance."
+                  }
+                }
+              },
+              "discover_module_paths": {
+                "name": "discover_module_paths",
+                "kind": "function",
+                "path": "docforge.cli.mcp.logic.discover_module_paths",
+                "signature": "<bound method Alias.signature of Alias('discover_module_paths', 'docforge.loaders.discover_module_paths')>",
+                "docstring": "Discover all Python modules under a package via filesystem traversal.\n\nRules:\n- Directory with __init__.py is treated as a package.\n- Any .py file is treated as a module.\n- All paths are converted to dotted module paths.\n\nArgs:\n    module_name: The name of the package to discover.\n    project_root: The root directory of the project. Defaults to current working directory.\n\nReturns:\n    A sorted list of dotted module paths."
+              },
+              "MCPRenderer": {
+                "name": "MCPRenderer",
+                "kind": "class",
+                "path": "docforge.cli.mcp.logic.MCPRenderer",
+                "signature": "<bound method Alias.signature of Alias('MCPRenderer', 'docforge.renderers.MCPRenderer')>",
+                "docstring": "Renderer that emits MCP-native JSON resources from docforge models.",
+                "members": {
+                  "name": {
+                    "name": "name",
+                    "kind": "attribute",
+                    "path": "docforge.cli.mcp.logic.MCPRenderer.name",
+                    "signature": "<bound method Alias.signature of Alias('name', 'docforge.renderers.mcp_renderer.MCPRenderer.name')>",
+                    "docstring": null
+                  },
+                  "generate_sources": {
+                    "name": "generate_sources",
+                    "kind": "function",
+                    "path": "docforge.cli.mcp.logic.MCPRenderer.generate_sources",
+                    "signature": "<bound method Alias.signature of Alias('generate_sources', 'docforge.renderers.mcp_renderer.MCPRenderer.generate_sources')>",
+                    "docstring": "Generate MCP-compatible JSON resources and navigation for the project."
+                  }
+                }
+              },
+              "MCPServer": {
+                "name": "MCPServer",
+                "kind": "class",
+                "path": "docforge.cli.mcp.logic.MCPServer",
+                "signature": "<bound method Alias.signature of Alias('MCPServer', 'docforge.servers.MCPServer')>",
+                "docstring": "MCP server for serving a pre-built MCP documentation bundle.",
+                "members": {
+                  "mcp_root": {
+                    "name": "mcp_root",
+                    "kind": "attribute",
+                    "path": "docforge.cli.mcp.logic.MCPServer.mcp_root",
+                    "signature": "<bound method Alias.signature of Alias('mcp_root', 'docforge.servers.mcp_server.MCPServer.mcp_root')>",
+                    "docstring": null
+                  },
+                  "app": {
+                    "name": "app",
+                    "kind": "attribute",
+                    "path": "docforge.cli.mcp.logic.MCPServer.app",
+                    "signature": "<bound method Alias.signature of Alias('app', 'docforge.servers.mcp_server.MCPServer.app')>",
+                    "docstring": null
+                  },
+                  "run": {
+                    "name": "run",
+                    "kind": "function",
+                    "path": "docforge.cli.mcp.logic.MCPServer.run",
+                    "signature": "<bound method Alias.signature of Alias('run', 'docforge.servers.mcp_server.MCPServer.run')>",
+                    "docstring": "Start the MCP server.\n\nArgs:\n    transport: MCP transport (default: streamable-http)"
+                  }
+                }
+              },
+              "generate_resources": {
+                "name": "generate_resources",
+                "kind": "function",
+                "path": "docforge.cli.mcp.logic.generate_resources",
+                "signature": "<bound method Function.signature of Function('generate_resources', 7, 16)>",
+                "docstring": "Generate MCP-compatible documentation resources."
+              },
+              "serve": {
+                "name": "serve",
+                "kind": "function",
+                "path": "docforge.cli.mcp.logic.serve",
+                "signature": "<bound method Function.signature of Function('serve', 18, 39)>",
+                "docstring": "Serve MCP documentation."
+              }
+            }
           }
         }
       },
@@ -185,93 +517,155 @@
         "kind": "module",
         "path": "docforge.cli.mkdocs",
         "signature": null,
-        "docstring": "This module contains the 'mkdocs' CLI command, which orchestrates the generation\nof the main mkdocs.yml configuration file.",
+        "docstring": null,
+        "members": {
+          "logic": {
+            "name": "logic",
+            "kind": "module",
+            "path": "docforge.cli.mkdocs.logic",
+            "signature": null,
+            "docstring": null,
             "members": {
               "Path": {
                 "name": "Path",
                 "kind": "alias",
-            "path": "docforge.cli.mkdocs.Path",
+                "path": "docforge.cli.mkdocs.logic.Path",
                 "signature": "<bound method Alias.signature of Alias('Path', 'pathlib.Path')>",
                 "docstring": null
               },
               "resources": {
                 "name": "resources",
                 "kind": "alias",
-            "path": "docforge.cli.mkdocs.resources",
+                "path": "docforge.cli.mkdocs.logic.resources",
                 "signature": "<bound method Alias.signature of Alias('resources', 'importlib.resources')>",
                 "docstring": null
               },
               "click": {
                 "name": "click",
                 "kind": "alias",
-            "path": "docforge.cli.mkdocs.click",
+                "path": "docforge.cli.mkdocs.logic.click",
                 "signature": "<bound method Alias.signature of Alias('click', 'click')>",
                 "docstring": null
               },
               "yaml": {
                 "name": "yaml",
                 "kind": "alias",
-            "path": "docforge.cli.mkdocs.yaml",
+                "path": "docforge.cli.mkdocs.logic.yaml",
                 "signature": "<bound method Alias.signature of Alias('yaml', 'yaml')>",
                 "docstring": null
               },
+              "GriffeLoader": {
+                "name": "GriffeLoader",
+                "kind": "class",
+                "path": "docforge.cli.mkdocs.logic.GriffeLoader",
+                "signature": "<bound method Alias.signature of Alias('GriffeLoader', 'docforge.loaders.GriffeLoader')>",
+                "docstring": "Loads Python modules and extracts documentation using the Griffe introspection engine.",
+                "members": {
+                  "load_project": {
+                    "name": "load_project",
+                    "kind": "function",
+                    "path": "docforge.cli.mkdocs.logic.GriffeLoader.load_project",
+                    "signature": "<bound method Alias.signature of Alias('load_project', 'docforge.loaders.griffe_loader.GriffeLoader.load_project')>",
+                    "docstring": "Load multiple modules and combine them into a single Project models.\n\nArgs:\n    module_paths: A list of dotted paths to the modules to load.\n    project_name: Optional name for the project. Defaults to the first module name.\n    skip_import_errors: If True, modules that fail to import will be skipped.\n\nReturns:\n    A Project instance containing the loaded modules."
+                  },
+                  "load_module": {
+                    "name": "load_module",
+                    "kind": "function",
+                    "path": "docforge.cli.mkdocs.logic.GriffeLoader.load_module",
+                    "signature": "<bound method Alias.signature of Alias('load_module', 'docforge.loaders.griffe_loader.GriffeLoader.load_module')>",
+                    "docstring": "Load a single module and convert its introspection data into the docforge models.\n\nArgs:\n    path: The dotted path of the module to load.\n\nReturns:\n    A Module instance."
+                  }
+                }
+              },
+              "discover_module_paths": {
+                "name": "discover_module_paths",
+                "kind": "function",
+                "path": "docforge.cli.mkdocs.logic.discover_module_paths",
+                "signature": "<bound method Alias.signature of Alias('discover_module_paths', 'docforge.loaders.discover_module_paths')>",
+                "docstring": "Discover all Python modules under a package via filesystem traversal.\n\nRules:\n- Directory with __init__.py is treated as a package.\n- Any .py file is treated as a module.\n- All paths are converted to dotted module paths.\n\nArgs:\n    module_name: The name of the package to discover.\n    project_root: The root directory of the project. Defaults to current working directory.\n\nReturns:\n    A sorted list of dotted module paths."
+              },
+              "MkDocsRenderer": {
+                "name": "MkDocsRenderer",
+                "kind": "class",
+                "path": "docforge.cli.mkdocs.logic.MkDocsRenderer",
+                "signature": "<bound method Alias.signature of Alias('MkDocsRenderer', 'docforge.renderers.MkDocsRenderer')>",
+                "docstring": "Renderer that generates Markdown source files formatted for the MkDocs\n'mkdocstrings' plugin.",
+                "members": {
+                  "name": {
+                    "name": "name",
+                    "kind": "attribute",
+                    "path": "docforge.cli.mkdocs.logic.MkDocsRenderer.name",
+                    "signature": "<bound method Alias.signature of Alias('name', 'docforge.renderers.mkdocs_renderer.MkDocsRenderer.name')>",
+                    "docstring": null
+                  },
+                  "generate_sources": {
+                    "name": "generate_sources",
+                    "kind": "function",
+                    "path": "docforge.cli.mkdocs.logic.MkDocsRenderer.generate_sources",
+                    "signature": "<bound method Alias.signature of Alias('generate_sources', 'docforge.renderers.mkdocs_renderer.MkDocsRenderer.generate_sources')>",
+                    "docstring": "Produce a set of Markdown files in the output directory based on the\nprovided Project models.\n\nArgs:\n    project: The project models to render.\n    out_dir: Target directory for documentation files."
+                  }
+                }
+              },
               "load_nav_spec": {
                 "name": "load_nav_spec",
                 "kind": "function",
-            "path": "docforge.cli.mkdocs.load_nav_spec",
+                "path": "docforge.cli.mkdocs.logic.load_nav_spec",
                 "signature": "<bound method Alias.signature of Alias('load_nav_spec', 'docforge.nav.load_nav_spec')>",
                 "docstring": "Utility function to load a NavSpec from a file.\n\nArgs:\n    path: Path to the navigation specification file.\n\nReturns:\n    A loaded NavSpec instance."
               },
               "resolve_nav": {
                 "name": "resolve_nav",
                 "kind": "function",
-            "path": "docforge.cli.mkdocs.resolve_nav",
+                "path": "docforge.cli.mkdocs.logic.resolve_nav",
                 "signature": "<bound method Alias.signature of Alias('resolve_nav', 'docforge.nav.resolve_nav')>",
                 "docstring": "Create a ResolvedNav by processing a NavSpec against the filesystem.\nThis expands globs and validates the existence of referenced files.\n\nArgs:\n    spec: The navigation specification to resolve.\n    docs_root: The root directory for documentation files.\n\nReturns:\n    A ResolvedNav instance.\n\nRaises:\n    FileNotFoundError: If a pattern doesn't match any files or the docs_root doesn't exist."
               },
               "MkDocsNavEmitter": {
                 "name": "MkDocsNavEmitter",
                 "kind": "class",
-            "path": "docforge.cli.mkdocs.MkDocsNavEmitter",
+                "path": "docforge.cli.mkdocs.logic.MkDocsNavEmitter",
                 "signature": "<bound method Alias.signature of Alias('MkDocsNavEmitter', 'docforge.nav.MkDocsNavEmitter')>",
                 "docstring": "Emitter responsible for transforming a ResolvedNav into an MkDocs-compatible\nnavigation structure.",
                 "members": {
                   "emit": {
                     "name": "emit",
                     "kind": "function",
-                "path": "docforge.cli.mkdocs.MkDocsNavEmitter.emit",
+                    "path": "docforge.cli.mkdocs.logic.MkDocsNavEmitter.emit",
                     "signature": "<bound method Alias.signature of Alias('emit', 'docforge.nav.mkdocs.MkDocsNavEmitter.emit')>",
                     "docstring": "Generate a list of navigation entries for mkdocs.yml.\n\nArgs:\n    nav: The resolved navigation data.\n\nReturns:\n    A list of dictionary mappings representing the MkDocs navigation."
                   }
                 }
               },
-          "mkdocs_cmd": {
-            "name": "mkdocs_cmd",
+              "generate_sources": {
+                "name": "generate_sources",
                 "kind": "function",
-            "path": "docforge.cli.mkdocs.mkdocs_cmd",
-            "signature": "<bound method Function.signature of Function('mkdocs_cmd', 42, 116)>",
-            "docstring": "Generate an mkdocs.yml configuration file by combining a template with\nthe navigation structure resolved from a docforge.nav.yml file.\n\nArgs:\n    docs_dir: Path to the directory containing documentation Markdown files.\n    nav_file: Path to the docforge.nav.yml specification.\n    template: Optional path to an mkdocs.yml template.\n    out: Path where the final mkdocs.yml will be written.\n    site_name: The name of the documentation site."
+                "path": "docforge.cli.mkdocs.logic.generate_sources",
+                "signature": "<bound method Function.signature of Function('generate_sources', 9, 18)>",
+                "docstring": "Generate Markdown source files for the specified module."
               },
-          "Any": {
-            "name": "Any",
-            "kind": "alias",
-            "path": "docforge.cli.mkdocs.Any",
-            "signature": "<bound method Alias.signature of Alias('Any', 'typing.Any')>",
-            "docstring": null
+              "generate_config": {
+                "name": "generate_config",
+                "kind": "function",
+                "path": "docforge.cli.mkdocs.logic.generate_config",
+                "signature": "<bound method Function.signature of Function('generate_config', 20, 47)>",
+                "docstring": "Generate an mkdocs.yml configuration file."
               },
-          "Dict": {
-            "name": "Dict",
-            "kind": "alias",
-            "path": "docforge.cli.mkdocs.Dict",
-            "signature": "<bound method Alias.signature of Alias('Dict', 'typing.Dict')>",
-            "docstring": null
+              "build": {
+                "name": "build",
+                "kind": "function",
+                "path": "docforge.cli.mkdocs.logic.build",
+                "signature": "<bound method Function.signature of Function('build', 49, 59)>",
+                "docstring": "Build the documentation site using MkDocs."
               },
-          "Optional": {
-            "name": "Optional",
-            "kind": "alias",
-            "path": "docforge.cli.mkdocs.Optional",
-            "signature": "<bound method Alias.signature of Alias('Optional', 'typing.Optional')>",
-            "docstring": null
+              "serve": {
+                "name": "serve",
+                "kind": "function",
+                "path": "docforge.cli.mkdocs.logic.serve",
+                "signature": "<bound method Function.signature of Function('serve', 61, 69)>",
+                "docstring": "Serve the documentation site with live-reload using MkDocs."
+              }
+            }
           }
         }
       }

mcp_docs/modules/docforge.cli.main.json

@@ -2,173 +2,20 @@
   "module": "docforge.cli.main",
   "content": {
     "path": "docforge.cli.main",
-    "docstring": "Main entry point for the doc-forge CLI. This module defines the core command\ngroup and the 'tree', 'generate', 'build', and 'serve' commands.",
+    "docstring": "Main entry point for the doc-forge CLI.",
     "objects": {
-      "Path": {
-        "name": "Path",
-        "kind": "alias",
-        "path": "docforge.cli.main.Path",
-        "signature": "<bound method Alias.signature of Alias('Path', 'pathlib.Path')>",
-        "docstring": null
-      },
-      "Sequence": {
-        "name": "Sequence",
-        "kind": "alias",
-        "path": "docforge.cli.main.Sequence",
-        "signature": "<bound method Alias.signature of Alias('Sequence', 'typing.Sequence')>",
-        "docstring": null
-      },
-      "Optional": {
-        "name": "Optional",
-        "kind": "alias",
-        "path": "docforge.cli.main.Optional",
-        "signature": "<bound method Alias.signature of Alias('Optional', 'typing.Optional')>",
-        "docstring": null
-      },
-      "click": {
-        "name": "click",
-        "kind": "alias",
-        "path": "docforge.cli.main.click",
-        "signature": "<bound method Alias.signature of Alias('click', 'click')>",
-        "docstring": null
-      },
-      "GriffeLoader": {
-        "name": "GriffeLoader",
-        "kind": "class",
-        "path": "docforge.cli.main.GriffeLoader",
-        "signature": "<bound method Alias.signature of Alias('GriffeLoader', 'docforge.loaders.GriffeLoader')>",
-        "docstring": "Loads Python modules and extracts documentation using the Griffe introspection engine.",
-        "members": {
-          "load_project": {
-            "name": "load_project",
-            "kind": "function",
-            "path": "docforge.cli.main.GriffeLoader.load_project",
-            "signature": "<bound method Alias.signature of Alias('load_project', 'docforge.loaders.griffe_loader.GriffeLoader.load_project')>",
-            "docstring": "Load multiple modules and combine them into a single Project models.\n\nArgs:\n    module_paths: A list of dotted paths to the modules to load.\n    project_name: Optional name for the project. Defaults to the first module name.\n    skip_import_errors: If True, modules that fail to import will be skipped.\n\nReturns:\n    A Project instance containing the loaded modules."
-          },
-          "load_module": {
-            "name": "load_module",
-            "kind": "function",
-            "path": "docforge.cli.main.GriffeLoader.load_module",
-            "signature": "<bound method Alias.signature of Alias('load_module', 'docforge.loaders.griffe_loader.GriffeLoader.load_module')>",
-            "docstring": "Load a single module and convert its introspection data into the docforge models.\n\nArgs:\n    path: The dotted path of the module to load.\n\nReturns:\n    A Module instance."
-          }
-        }
-      },
-      "discover_module_paths": {
-        "name": "discover_module_paths",
-        "kind": "function",
-        "path": "docforge.cli.main.discover_module_paths",
-        "signature": "<bound method Alias.signature of Alias('discover_module_paths', 'docforge.loaders.discover_module_paths')>",
-        "docstring": "Discover all Python modules under a package via filesystem traversal.\n\nRules:\n- Directory with __init__.py is treated as a package.\n- Any .py file is treated as a module.\n- All paths are converted to dotted module paths.\n\nArgs:\n    module_name: The name of the package to discover.\n    project_root: The root directory of the project. Defaults to current working directory.\n\nReturns:\n    A sorted list of dotted module paths."
-      },
-      "MkDocsRenderer": {
-        "name": "MkDocsRenderer",
-        "kind": "class",
-        "path": "docforge.cli.main.MkDocsRenderer",
-        "signature": "<bound method Alias.signature of Alias('MkDocsRenderer', 'docforge.renderers.MkDocsRenderer')>",
-        "docstring": "Renderer that generates Markdown source files formatted for the MkDocs\n'mkdocstrings' plugin.",
-        "members": {
-          "name": {
-            "name": "name",
-            "kind": "attribute",
-            "path": "docforge.cli.main.MkDocsRenderer.name",
-            "signature": "<bound method Alias.signature of Alias('name', 'docforge.renderers.mkdocs_renderer.MkDocsRenderer.name')>",
-            "docstring": null
-          },
-          "generate_sources": {
-            "name": "generate_sources",
-            "kind": "function",
-            "path": "docforge.cli.main.MkDocsRenderer.generate_sources",
-            "signature": "<bound method Alias.signature of Alias('generate_sources', 'docforge.renderers.mkdocs_renderer.MkDocsRenderer.generate_sources')>",
-            "docstring": "Produce a set of Markdown files in the output directory based on the\nprovided Project models.\n\nArgs:\n    project: The project models to render.\n    out_dir: Target directory for documentation files."
-          }
-        }
-      },
-      "MCPRenderer": {
-        "name": "MCPRenderer",
-        "kind": "class",
-        "path": "docforge.cli.main.MCPRenderer",
-        "signature": "<bound method Alias.signature of Alias('MCPRenderer', 'docforge.renderers.MCPRenderer')>",
-        "docstring": "Renderer that emits MCP-native JSON resources from docforge models.",
-        "members": {
-          "name": {
-            "name": "name",
-            "kind": "attribute",
-            "path": "docforge.cli.main.MCPRenderer.name",
-            "signature": "<bound method Alias.signature of Alias('name', 'docforge.renderers.mcp_renderer.MCPRenderer.name')>",
-            "docstring": null
-          },
-          "generate_sources": {
-            "name": "generate_sources",
-            "kind": "function",
-            "path": "docforge.cli.main.MCPRenderer.generate_sources",
-            "signature": "<bound method Alias.signature of Alias('generate_sources', 'docforge.renderers.mcp_renderer.MCPRenderer.generate_sources')>",
-            "docstring": "Generate MCP-compatible JSON resources and navigation for the project."
-          }
-        }
-      },
-      "mkdocs_cmd": {
-        "name": "mkdocs_cmd",
-        "kind": "function",
-        "path": "docforge.cli.main.mkdocs_cmd",
-        "signature": "<bound method Alias.signature of Alias('mkdocs_cmd', 'docforge.cli.mkdocs.mkdocs_cmd')>",
-        "docstring": "Generate an mkdocs.yml configuration file by combining a template with\nthe navigation structure resolved from a docforge.nav.yml file.\n\nArgs:\n    docs_dir: Path to the directory containing documentation Markdown files.\n    nav_file: Path to the docforge.nav.yml specification.\n    template: Optional path to an mkdocs.yml template.\n    out: Path where the final mkdocs.yml will be written.\n    site_name: The name of the documentation site."
-      },
       "cli": {
         "name": "cli",
         "kind": "function",
         "path": "docforge.cli.main.cli",
-        "signature": "<bound method Function.signature of Function('cli', 16, 22)>",
+        "signature": "<bound method Alias.signature of Alias('cli', 'docforge.cli.commands.cli')>",
         "docstring": "doc-forge CLI: A tool for introspecting Python projects and generating\ndocumentation."
       },
-      "tree": {
-        "name": "tree",
-        "kind": "function",
-        "path": "docforge.cli.main.tree",
-        "signature": "<bound method Function.signature of Function('tree', 31, 62)>",
-        "docstring": "Visualize the project structure including modules and their members.\n\nArgs:\n    modules: List of module paths to introspect.\n    project_name: Optional project name override."
-      },
-      "generate": {
-        "name": "generate",
-        "kind": "function",
-        "path": "docforge.cli.main.generate",
-        "signature": "<bound method Function.signature of Function('generate', 82, 122)>",
-        "docstring": "Generate Markdown source files for the specified module.\n\nArgs:\n    module: The primary module path to document.\n    project_name: Optional project name override.\n    docs_dir: Directory where documentation sources will be written."
-      },
-      "generate_mcp": {
-        "name": "generate_mcp",
-        "kind": "function",
-        "path": "docforge.cli.main.generate_mcp",
-        "signature": "<bound method Function.signature of Function('generate_mcp', 129, 168)>",
-        "docstring": "Generate MCP-compatible documentation resources for the specified module.\n\nArgs:\n    module: The primary module path to document.\n    project_name: Optional project name override.\n    out_dir: Directory where MCP resources will be written."
-      },
-      "build": {
-        "name": "build",
-        "kind": "function",
-        "path": "docforge.cli.main.build",
-        "signature": "<bound method Function.signature of Function('build', 175, 196)>",
-        "docstring": "Build the documentation site using MkDocs.\n\nArgs:\n    mkdocs_yml: Path to the mkdocs.yml configuration file."
-      },
-      "serve_mcp": {
-        "name": "serve_mcp",
-        "kind": "function",
-        "path": "docforge.cli.main.serve_mcp",
-        "signature": "<bound method Function.signature of Function('serve_mcp', 203, 230)>",
-        "docstring": "Serve MCP documentation from the local mcp_docs directory."
-      },
-      "serve": {
-        "name": "serve",
-        "kind": "function",
-        "path": "docforge.cli.main.serve",
-        "signature": "<bound method Function.signature of Function('serve', 237, 260)>",
-        "docstring": "Serve the documentation site with live-reload using MkDocs.\n\nArgs:\n    mkdocs_yml: Path to the mkdocs.yml configuration file."
-      },
       "main": {
         "name": "main",
         "kind": "function",
         "path": "docforge.cli.main.main",
-        "signature": "<bound method Function.signature of Function('main', 267, 271)>",
+        "signature": "<bound method Function.signature of Function('main', 6, 10)>",
         "docstring": "CLI Entry point. Boots the click application."
       }
     }

mcp_docs/modules/docforge.cli.mcp.json

@@ -0,0 +1,129 @@
+{
+  "module": "docforge.cli.mcp",
+  "content": {
+    "path": "docforge.cli.mcp",
+    "docstring": null,
+    "objects": {
+      "logic": {
+        "name": "logic",
+        "kind": "module",
+        "path": "docforge.cli.mcp.logic",
+        "signature": null,
+        "docstring": null,
+        "members": {
+          "Path": {
+            "name": "Path",
+            "kind": "alias",
+            "path": "docforge.cli.mcp.logic.Path",
+            "signature": "<bound method Alias.signature of Alias('Path', 'pathlib.Path')>",
+            "docstring": null
+          },
+          "click": {
+            "name": "click",
+            "kind": "alias",
+            "path": "docforge.cli.mcp.logic.click",
+            "signature": "<bound method Alias.signature of Alias('click', 'click')>",
+            "docstring": null
+          },
+          "GriffeLoader": {
+            "name": "GriffeLoader",
+            "kind": "class",
+            "path": "docforge.cli.mcp.logic.GriffeLoader",
+            "signature": "<bound method Alias.signature of Alias('GriffeLoader', 'docforge.loaders.GriffeLoader')>",
+            "docstring": "Loads Python modules and extracts documentation using the Griffe introspection engine.",
+            "members": {
+              "load_project": {
+                "name": "load_project",
+                "kind": "function",
+                "path": "docforge.cli.mcp.logic.GriffeLoader.load_project",
+                "signature": "<bound method Alias.signature of Alias('load_project', 'docforge.loaders.griffe_loader.GriffeLoader.load_project')>",
+                "docstring": "Load multiple modules and combine them into a single Project models.\n\nArgs:\n    module_paths: A list of dotted paths to the modules to load.\n    project_name: Optional name for the project. Defaults to the first module name.\n    skip_import_errors: If True, modules that fail to import will be skipped.\n\nReturns:\n    A Project instance containing the loaded modules."
+              },
+              "load_module": {
+                "name": "load_module",
+                "kind": "function",
+                "path": "docforge.cli.mcp.logic.GriffeLoader.load_module",
+                "signature": "<bound method Alias.signature of Alias('load_module', 'docforge.loaders.griffe_loader.GriffeLoader.load_module')>",
+                "docstring": "Load a single module and convert its introspection data into the docforge models.\n\nArgs:\n    path: The dotted path of the module to load.\n\nReturns:\n    A Module instance."
+              }
+            }
+          },
+          "discover_module_paths": {
+            "name": "discover_module_paths",
+            "kind": "function",
+            "path": "docforge.cli.mcp.logic.discover_module_paths",
+            "signature": "<bound method Alias.signature of Alias('discover_module_paths', 'docforge.loaders.discover_module_paths')>",
+            "docstring": "Discover all Python modules under a package via filesystem traversal.\n\nRules:\n- Directory with __init__.py is treated as a package.\n- Any .py file is treated as a module.\n- All paths are converted to dotted module paths.\n\nArgs:\n    module_name: The name of the package to discover.\n    project_root: The root directory of the project. Defaults to current working directory.\n\nReturns:\n    A sorted list of dotted module paths."
+          },
+          "MCPRenderer": {
+            "name": "MCPRenderer",
+            "kind": "class",
+            "path": "docforge.cli.mcp.logic.MCPRenderer",
+            "signature": "<bound method Alias.signature of Alias('MCPRenderer', 'docforge.renderers.MCPRenderer')>",
+            "docstring": "Renderer that emits MCP-native JSON resources from docforge models.",
+            "members": {
+              "name": {
+                "name": "name",
+                "kind": "attribute",
+                "path": "docforge.cli.mcp.logic.MCPRenderer.name",
+                "signature": "<bound method Alias.signature of Alias('name', 'docforge.renderers.mcp_renderer.MCPRenderer.name')>",
+                "docstring": null
+              },
+              "generate_sources": {
+                "name": "generate_sources",
+                "kind": "function",
+                "path": "docforge.cli.mcp.logic.MCPRenderer.generate_sources",
+                "signature": "<bound method Alias.signature of Alias('generate_sources', 'docforge.renderers.mcp_renderer.MCPRenderer.generate_sources')>",
+                "docstring": "Generate MCP-compatible JSON resources and navigation for the project."
+              }
+            }
+          },
+          "MCPServer": {
+            "name": "MCPServer",
+            "kind": "class",
+            "path": "docforge.cli.mcp.logic.MCPServer",
+            "signature": "<bound method Alias.signature of Alias('MCPServer', 'docforge.servers.MCPServer')>",
+            "docstring": "MCP server for serving a pre-built MCP documentation bundle.",
+            "members": {
+              "mcp_root": {
+                "name": "mcp_root",
+                "kind": "attribute",
+                "path": "docforge.cli.mcp.logic.MCPServer.mcp_root",
+                "signature": "<bound method Alias.signature of Alias('mcp_root', 'docforge.servers.mcp_server.MCPServer.mcp_root')>",
+                "docstring": null
+              },
+              "app": {
+                "name": "app",
+                "kind": "attribute",
+                "path": "docforge.cli.mcp.logic.MCPServer.app",
+                "signature": "<bound method Alias.signature of Alias('app', 'docforge.servers.mcp_server.MCPServer.app')>",
+                "docstring": null
+              },
+              "run": {
+                "name": "run",
+                "kind": "function",
+                "path": "docforge.cli.mcp.logic.MCPServer.run",
+                "signature": "<bound method Alias.signature of Alias('run', 'docforge.servers.mcp_server.MCPServer.run')>",
+                "docstring": "Start the MCP server.\n\nArgs:\n    transport: MCP transport (default: streamable-http)"
+              }
+            }
+          },
+          "generate_resources": {
+            "name": "generate_resources",
+            "kind": "function",
+            "path": "docforge.cli.mcp.logic.generate_resources",
+            "signature": "<bound method Function.signature of Function('generate_resources', 7, 16)>",
+            "docstring": "Generate MCP-compatible documentation resources."
+          },
+          "serve": {
+            "name": "serve",
+            "kind": "function",
+            "path": "docforge.cli.mcp.logic.serve",
+            "signature": "<bound method Function.signature of Function('serve', 18, 39)>",
+            "docstring": "Serve MCP documentation."
+          }
+        }
+      }
+    }
+  }
+}

mcp_docs/modules/docforge.cli.mcp.logic.json

@@ -0,0 +1,120 @@
+{
+  "module": "docforge.cli.mcp.logic",
+  "content": {
+    "path": "docforge.cli.mcp.logic",
+    "docstring": null,
+    "objects": {
+      "Path": {
+        "name": "Path",
+        "kind": "alias",
+        "path": "docforge.cli.mcp.logic.Path",
+        "signature": "<bound method Alias.signature of Alias('Path', 'pathlib.Path')>",
+        "docstring": null
+      },
+      "click": {
+        "name": "click",
+        "kind": "alias",
+        "path": "docforge.cli.mcp.logic.click",
+        "signature": "<bound method Alias.signature of Alias('click', 'click')>",
+        "docstring": null
+      },
+      "GriffeLoader": {
+        "name": "GriffeLoader",
+        "kind": "class",
+        "path": "docforge.cli.mcp.logic.GriffeLoader",
+        "signature": "<bound method Alias.signature of Alias('GriffeLoader', 'docforge.loaders.GriffeLoader')>",
+        "docstring": "Loads Python modules and extracts documentation using the Griffe introspection engine.",
+        "members": {
+          "load_project": {
+            "name": "load_project",
+            "kind": "function",
+            "path": "docforge.cli.mcp.logic.GriffeLoader.load_project",
+            "signature": "<bound method Alias.signature of Alias('load_project', 'docforge.loaders.griffe_loader.GriffeLoader.load_project')>",
+            "docstring": "Load multiple modules and combine them into a single Project models.\n\nArgs:\n    module_paths: A list of dotted paths to the modules to load.\n    project_name: Optional name for the project. Defaults to the first module name.\n    skip_import_errors: If True, modules that fail to import will be skipped.\n\nReturns:\n    A Project instance containing the loaded modules."
+          },
+          "load_module": {
+            "name": "load_module",
+            "kind": "function",
+            "path": "docforge.cli.mcp.logic.GriffeLoader.load_module",
+            "signature": "<bound method Alias.signature of Alias('load_module', 'docforge.loaders.griffe_loader.GriffeLoader.load_module')>",
+            "docstring": "Load a single module and convert its introspection data into the docforge models.\n\nArgs:\n    path: The dotted path of the module to load.\n\nReturns:\n    A Module instance."
+          }
+        }
+      },
+      "discover_module_paths": {
+        "name": "discover_module_paths",
+        "kind": "function",
+        "path": "docforge.cli.mcp.logic.discover_module_paths",
+        "signature": "<bound method Alias.signature of Alias('discover_module_paths', 'docforge.loaders.discover_module_paths')>",
+        "docstring": "Discover all Python modules under a package via filesystem traversal.\n\nRules:\n- Directory with __init__.py is treated as a package.\n- Any .py file is treated as a module.\n- All paths are converted to dotted module paths.\n\nArgs:\n    module_name: The name of the package to discover.\n    project_root: The root directory of the project. Defaults to current working directory.\n\nReturns:\n    A sorted list of dotted module paths."
+      },
+      "MCPRenderer": {
+        "name": "MCPRenderer",
+        "kind": "class",
+        "path": "docforge.cli.mcp.logic.MCPRenderer",
+        "signature": "<bound method Alias.signature of Alias('MCPRenderer', 'docforge.renderers.MCPRenderer')>",
+        "docstring": "Renderer that emits MCP-native JSON resources from docforge models.",
+        "members": {
+          "name": {
+            "name": "name",
+            "kind": "attribute",
+            "path": "docforge.cli.mcp.logic.MCPRenderer.name",
+            "signature": "<bound method Alias.signature of Alias('name', 'docforge.renderers.mcp_renderer.MCPRenderer.name')>",
+            "docstring": null
+          },
+          "generate_sources": {
+            "name": "generate_sources",
+            "kind": "function",
+            "path": "docforge.cli.mcp.logic.MCPRenderer.generate_sources",
+            "signature": "<bound method Alias.signature of Alias('generate_sources', 'docforge.renderers.mcp_renderer.MCPRenderer.generate_sources')>",
+            "docstring": "Generate MCP-compatible JSON resources and navigation for the project."
+          }
+        }
+      },
+      "MCPServer": {
+        "name": "MCPServer",
+        "kind": "class",
+        "path": "docforge.cli.mcp.logic.MCPServer",
+        "signature": "<bound method Alias.signature of Alias('MCPServer', 'docforge.servers.MCPServer')>",
+        "docstring": "MCP server for serving a pre-built MCP documentation bundle.",
+        "members": {
+          "mcp_root": {
+            "name": "mcp_root",
+            "kind": "attribute",
+            "path": "docforge.cli.mcp.logic.MCPServer.mcp_root",
+            "signature": "<bound method Alias.signature of Alias('mcp_root', 'docforge.servers.mcp_server.MCPServer.mcp_root')>",
+            "docstring": null
+          },
+          "app": {
+            "name": "app",
+            "kind": "attribute",
+            "path": "docforge.cli.mcp.logic.MCPServer.app",
+            "signature": "<bound method Alias.signature of Alias('app', 'docforge.servers.mcp_server.MCPServer.app')>",
+            "docstring": null
+          },
+          "run": {
+            "name": "run",
+            "kind": "function",
+            "path": "docforge.cli.mcp.logic.MCPServer.run",
+            "signature": "<bound method Alias.signature of Alias('run', 'docforge.servers.mcp_server.MCPServer.run')>",
+            "docstring": "Start the MCP server.\n\nArgs:\n    transport: MCP transport (default: streamable-http)"
+          }
+        }
+      },
+      "generate_resources": {
+        "name": "generate_resources",
+        "kind": "function",
+        "path": "docforge.cli.mcp.logic.generate_resources",
+        "signature": "<bound method Function.signature of Function('generate_resources', 7, 16)>",
+        "docstring": "Generate MCP-compatible documentation resources."
+      },
+      "serve": {
+        "name": "serve",
+        "kind": "function",
+        "path": "docforge.cli.mcp.logic.serve",
+        "signature": "<bound method Function.signature of Function('serve', 18, 39)>",
+        "docstring": "Serve MCP documentation."
+      }
+    }
+  }
+}

mcp_docs/modules/docforge.cli.mkdocs.json

@@ -2,93 +2,155 @@
   "module": "docforge.cli.mkdocs",
   "content": {
     "path": "docforge.cli.mkdocs",
-    "docstring": "This module contains the 'mkdocs' CLI command, which orchestrates the generation\nof the main mkdocs.yml configuration file.",
+    "docstring": null,
     "objects": {
+      "logic": {
+        "name": "logic",
+        "kind": "module",
+        "path": "docforge.cli.mkdocs.logic",
+        "signature": null,
+        "docstring": null,
+        "members": {
           "Path": {
             "name": "Path",
             "kind": "alias",
-        "path": "docforge.cli.mkdocs.Path",
+            "path": "docforge.cli.mkdocs.logic.Path",
             "signature": "<bound method Alias.signature of Alias('Path', 'pathlib.Path')>",
             "docstring": null
           },
           "resources": {
             "name": "resources",
             "kind": "alias",
-        "path": "docforge.cli.mkdocs.resources",
+            "path": "docforge.cli.mkdocs.logic.resources",
             "signature": "<bound method Alias.signature of Alias('resources', 'importlib.resources')>",
             "docstring": null
           },
           "click": {
             "name": "click",
             "kind": "alias",
-        "path": "docforge.cli.mkdocs.click",
+            "path": "docforge.cli.mkdocs.logic.click",
             "signature": "<bound method Alias.signature of Alias('click', 'click')>",
             "docstring": null
           },
           "yaml": {
             "name": "yaml",
             "kind": "alias",
-        "path": "docforge.cli.mkdocs.yaml",
+            "path": "docforge.cli.mkdocs.logic.yaml",
             "signature": "<bound method Alias.signature of Alias('yaml', 'yaml')>",
             "docstring": null
           },
+          "GriffeLoader": {
+            "name": "GriffeLoader",
+            "kind": "class",
+            "path": "docforge.cli.mkdocs.logic.GriffeLoader",
+            "signature": "<bound method Alias.signature of Alias('GriffeLoader', 'docforge.loaders.GriffeLoader')>",
+            "docstring": "Loads Python modules and extracts documentation using the Griffe introspection engine.",
+            "members": {
+              "load_project": {
+                "name": "load_project",
+                "kind": "function",
+                "path": "docforge.cli.mkdocs.logic.GriffeLoader.load_project",
+                "signature": "<bound method Alias.signature of Alias('load_project', 'docforge.loaders.griffe_loader.GriffeLoader.load_project')>",
+                "docstring": "Load multiple modules and combine them into a single Project models.\n\nArgs:\n    module_paths: A list of dotted paths to the modules to load.\n    project_name: Optional name for the project. Defaults to the first module name.\n    skip_import_errors: If True, modules that fail to import will be skipped.\n\nReturns:\n    A Project instance containing the loaded modules."
+              },
+              "load_module": {
+                "name": "load_module",
+                "kind": "function",
+                "path": "docforge.cli.mkdocs.logic.GriffeLoader.load_module",
+                "signature": "<bound method Alias.signature of Alias('load_module', 'docforge.loaders.griffe_loader.GriffeLoader.load_module')>",
+                "docstring": "Load a single module and convert its introspection data into the docforge models.\n\nArgs:\n    path: The dotted path of the module to load.\n\nReturns:\n    A Module instance."
+              }
+            }
+          },
+          "discover_module_paths": {
+            "name": "discover_module_paths",
+            "kind": "function",
+            "path": "docforge.cli.mkdocs.logic.discover_module_paths",
+            "signature": "<bound method Alias.signature of Alias('discover_module_paths', 'docforge.loaders.discover_module_paths')>",
+            "docstring": "Discover all Python modules under a package via filesystem traversal.\n\nRules:\n- Directory with __init__.py is treated as a package.\n- Any .py file is treated as a module.\n- All paths are converted to dotted module paths.\n\nArgs:\n    module_name: The name of the package to discover.\n    project_root: The root directory of the project. Defaults to current working directory.\n\nReturns:\n    A sorted list of dotted module paths."
+          },
+          "MkDocsRenderer": {
+            "name": "MkDocsRenderer",
+            "kind": "class",
+            "path": "docforge.cli.mkdocs.logic.MkDocsRenderer",
+            "signature": "<bound method Alias.signature of Alias('MkDocsRenderer', 'docforge.renderers.MkDocsRenderer')>",
+            "docstring": "Renderer that generates Markdown source files formatted for the MkDocs\n'mkdocstrings' plugin.",
+            "members": {
+              "name": {
+                "name": "name",
+                "kind": "attribute",
+                "path": "docforge.cli.mkdocs.logic.MkDocsRenderer.name",
+                "signature": "<bound method Alias.signature of Alias('name', 'docforge.renderers.mkdocs_renderer.MkDocsRenderer.name')>",
+                "docstring": null
+              },
+              "generate_sources": {
+                "name": "generate_sources",
+                "kind": "function",
+                "path": "docforge.cli.mkdocs.logic.MkDocsRenderer.generate_sources",
+                "signature": "<bound method Alias.signature of Alias('generate_sources', 'docforge.renderers.mkdocs_renderer.MkDocsRenderer.generate_sources')>",
+                "docstring": "Produce a set of Markdown files in the output directory based on the\nprovided Project models.\n\nArgs:\n    project: The project models to render.\n    out_dir: Target directory for documentation files."
+              }
+            }
+          },
           "load_nav_spec": {
             "name": "load_nav_spec",
             "kind": "function",
-        "path": "docforge.cli.mkdocs.load_nav_spec",
+            "path": "docforge.cli.mkdocs.logic.load_nav_spec",
             "signature": "<bound method Alias.signature of Alias('load_nav_spec', 'docforge.nav.load_nav_spec')>",
             "docstring": "Utility function to load a NavSpec from a file.\n\nArgs:\n    path: Path to the navigation specification file.\n\nReturns:\n    A loaded NavSpec instance."
           },
           "resolve_nav": {
             "name": "resolve_nav",
             "kind": "function",
-        "path": "docforge.cli.mkdocs.resolve_nav",
+            "path": "docforge.cli.mkdocs.logic.resolve_nav",
             "signature": "<bound method Alias.signature of Alias('resolve_nav', 'docforge.nav.resolve_nav')>",
             "docstring": "Create a ResolvedNav by processing a NavSpec against the filesystem.\nThis expands globs and validates the existence of referenced files.\n\nArgs:\n    spec: The navigation specification to resolve.\n    docs_root: The root directory for documentation files.\n\nReturns:\n    A ResolvedNav instance.\n\nRaises:\n    FileNotFoundError: If a pattern doesn't match any files or the docs_root doesn't exist."
           },
           "MkDocsNavEmitter": {
             "name": "MkDocsNavEmitter",
             "kind": "class",
-        "path": "docforge.cli.mkdocs.MkDocsNavEmitter",
+            "path": "docforge.cli.mkdocs.logic.MkDocsNavEmitter",
             "signature": "<bound method Alias.signature of Alias('MkDocsNavEmitter', 'docforge.nav.MkDocsNavEmitter')>",
             "docstring": "Emitter responsible for transforming a ResolvedNav into an MkDocs-compatible\nnavigation structure.",
             "members": {
               "emit": {
                 "name": "emit",
                 "kind": "function",
-            "path": "docforge.cli.mkdocs.MkDocsNavEmitter.emit",
+                "path": "docforge.cli.mkdocs.logic.MkDocsNavEmitter.emit",
                 "signature": "<bound method Alias.signature of Alias('emit', 'docforge.nav.mkdocs.MkDocsNavEmitter.emit')>",
                 "docstring": "Generate a list of navigation entries for mkdocs.yml.\n\nArgs:\n    nav: The resolved navigation data.\n\nReturns:\n    A list of dictionary mappings representing the MkDocs navigation."
               }
             }
           },
-      "mkdocs_cmd": {
-        "name": "mkdocs_cmd",
+          "generate_sources": {
+            "name": "generate_sources",
             "kind": "function",
-        "path": "docforge.cli.mkdocs.mkdocs_cmd",
-        "signature": "<bound method Function.signature of Function('mkdocs_cmd', 42, 116)>",
-        "docstring": "Generate an mkdocs.yml configuration file by combining a template with\nthe navigation structure resolved from a docforge.nav.yml file.\n\nArgs:\n    docs_dir: Path to the directory containing documentation Markdown files.\n    nav_file: Path to the docforge.nav.yml specification.\n    template: Optional path to an mkdocs.yml template.\n    out: Path where the final mkdocs.yml will be written.\n    site_name: The name of the documentation site."
+            "path": "docforge.cli.mkdocs.logic.generate_sources",
+            "signature": "<bound method Function.signature of Function('generate_sources', 9, 18)>",
+            "docstring": "Generate Markdown source files for the specified module."
           },
-      "Any": {
-        "name": "Any",
-        "kind": "alias",
-        "path": "docforge.cli.mkdocs.Any",
-        "signature": "<bound method Alias.signature of Alias('Any', 'typing.Any')>",
-        "docstring": null
+          "generate_config": {
+            "name": "generate_config",
+            "kind": "function",
+            "path": "docforge.cli.mkdocs.logic.generate_config",
+            "signature": "<bound method Function.signature of Function('generate_config', 20, 47)>",
+            "docstring": "Generate an mkdocs.yml configuration file."
           },
-      "Dict": {
-        "name": "Dict",
-        "kind": "alias",
-        "path": "docforge.cli.mkdocs.Dict",
-        "signature": "<bound method Alias.signature of Alias('Dict', 'typing.Dict')>",
-        "docstring": null
+          "build": {
+            "name": "build",
+            "kind": "function",
+            "path": "docforge.cli.mkdocs.logic.build",
+            "signature": "<bound method Function.signature of Function('build', 49, 59)>",
+            "docstring": "Build the documentation site using MkDocs."
           },
-      "Optional": {
-        "name": "Optional",
-        "kind": "alias",
-        "path": "docforge.cli.mkdocs.Optional",
-        "signature": "<bound method Alias.signature of Alias('Optional', 'typing.Optional')>",
-        "docstring": null
+          "serve": {
+            "name": "serve",
+            "kind": "function",
+            "path": "docforge.cli.mkdocs.logic.serve",
+            "signature": "<bound method Function.signature of Function('serve', 61, 69)>",
+            "docstring": "Serve the documentation site with live-reload using MkDocs."
+          }
+        }
       }
     }
   }

mcp_docs/modules/docforge.cli.mkdocs.logic.json

@@ -0,0 +1,148 @@
+{
+  "module": "docforge.cli.mkdocs.logic",
+  "content": {
+    "path": "docforge.cli.mkdocs.logic",
+    "docstring": null,
+    "objects": {
+      "Path": {
+        "name": "Path",
+        "kind": "alias",
+        "path": "docforge.cli.mkdocs.logic.Path",
+        "signature": "<bound method Alias.signature of Alias('Path', 'pathlib.Path')>",
+        "docstring": null
+      },
+      "resources": {
+        "name": "resources",
+        "kind": "alias",
+        "path": "docforge.cli.mkdocs.logic.resources",
+        "signature": "<bound method Alias.signature of Alias('resources', 'importlib.resources')>",
+        "docstring": null
+      },
+      "click": {
+        "name": "click",
+        "kind": "alias",
+        "path": "docforge.cli.mkdocs.logic.click",
+        "signature": "<bound method Alias.signature of Alias('click', 'click')>",
+        "docstring": null
+      },
+      "yaml": {
+        "name": "yaml",
+        "kind": "alias",
+        "path": "docforge.cli.mkdocs.logic.yaml",
+        "signature": "<bound method Alias.signature of Alias('yaml', 'yaml')>",
+        "docstring": null
+      },
+      "GriffeLoader": {
+        "name": "GriffeLoader",
+        "kind": "class",
+        "path": "docforge.cli.mkdocs.logic.GriffeLoader",
+        "signature": "<bound method Alias.signature of Alias('GriffeLoader', 'docforge.loaders.GriffeLoader')>",
+        "docstring": "Loads Python modules and extracts documentation using the Griffe introspection engine.",
+        "members": {
+          "load_project": {
+            "name": "load_project",
+            "kind": "function",
+            "path": "docforge.cli.mkdocs.logic.GriffeLoader.load_project",
+            "signature": "<bound method Alias.signature of Alias('load_project', 'docforge.loaders.griffe_loader.GriffeLoader.load_project')>",
+            "docstring": "Load multiple modules and combine them into a single Project models.\n\nArgs:\n    module_paths: A list of dotted paths to the modules to load.\n    project_name: Optional name for the project. Defaults to the first module name.\n    skip_import_errors: If True, modules that fail to import will be skipped.\n\nReturns:\n    A Project instance containing the loaded modules."
+          },
+          "load_module": {
+            "name": "load_module",
+            "kind": "function",
+            "path": "docforge.cli.mkdocs.logic.GriffeLoader.load_module",
+            "signature": "<bound method Alias.signature of Alias('load_module', 'docforge.loaders.griffe_loader.GriffeLoader.load_module')>",
+            "docstring": "Load a single module and convert its introspection data into the docforge models.\n\nArgs:\n    path: The dotted path of the module to load.\n\nReturns:\n    A Module instance."
+          }
+        }
+      },
+      "discover_module_paths": {
+        "name": "discover_module_paths",
+        "kind": "function",
+        "path": "docforge.cli.mkdocs.logic.discover_module_paths",
+        "signature": "<bound method Alias.signature of Alias('discover_module_paths', 'docforge.loaders.discover_module_paths')>",
+        "docstring": "Discover all Python modules under a package via filesystem traversal.\n\nRules:\n- Directory with __init__.py is treated as a package.\n- Any .py file is treated as a module.\n- All paths are converted to dotted module paths.\n\nArgs:\n    module_name: The name of the package to discover.\n    project_root: The root directory of the project. Defaults to current working directory.\n\nReturns:\n    A sorted list of dotted module paths."
+      },
+      "MkDocsRenderer": {
+        "name": "MkDocsRenderer",
+        "kind": "class",
+        "path": "docforge.cli.mkdocs.logic.MkDocsRenderer",
+        "signature": "<bound method Alias.signature of Alias('MkDocsRenderer', 'docforge.renderers.MkDocsRenderer')>",
+        "docstring": "Renderer that generates Markdown source files formatted for the MkDocs\n'mkdocstrings' plugin.",
+        "members": {
+          "name": {
+            "name": "name",
+            "kind": "attribute",
+            "path": "docforge.cli.mkdocs.logic.MkDocsRenderer.name",
+            "signature": "<bound method Alias.signature of Alias('name', 'docforge.renderers.mkdocs_renderer.MkDocsRenderer.name')>",
+            "docstring": null
+          },
+          "generate_sources": {
+            "name": "generate_sources",
+            "kind": "function",
+            "path": "docforge.cli.mkdocs.logic.MkDocsRenderer.generate_sources",
+            "signature": "<bound method Alias.signature of Alias('generate_sources', 'docforge.renderers.mkdocs_renderer.MkDocsRenderer.generate_sources')>",
+            "docstring": "Produce a set of Markdown files in the output directory based on the\nprovided Project models.\n\nArgs:\n    project: The project models to render.\n    out_dir: Target directory for documentation files."
+          }
+        }
+      },
+      "load_nav_spec": {
+        "name": "load_nav_spec",
+        "kind": "function",
+        "path": "docforge.cli.mkdocs.logic.load_nav_spec",
+        "signature": "<bound method Alias.signature of Alias('load_nav_spec', 'docforge.nav.load_nav_spec')>",
+        "docstring": "Utility function to load a NavSpec from a file.\n\nArgs:\n    path: Path to the navigation specification file.\n\nReturns:\n    A loaded NavSpec instance."
+      },
+      "resolve_nav": {
+        "name": "resolve_nav",
+        "kind": "function",
+        "path": "docforge.cli.mkdocs.logic.resolve_nav",
+        "signature": "<bound method Alias.signature of Alias('resolve_nav', 'docforge.nav.resolve_nav')>",
+        "docstring": "Create a ResolvedNav by processing a NavSpec against the filesystem.\nThis expands globs and validates the existence of referenced files.\n\nArgs:\n    spec: The navigation specification to resolve.\n    docs_root: The root directory for documentation files.\n\nReturns:\n    A ResolvedNav instance.\n\nRaises:\n    FileNotFoundError: If a pattern doesn't match any files or the docs_root doesn't exist."
+      },
+      "MkDocsNavEmitter": {
+        "name": "MkDocsNavEmitter",
+        "kind": "class",
+        "path": "docforge.cli.mkdocs.logic.MkDocsNavEmitter",
+        "signature": "<bound method Alias.signature of Alias('MkDocsNavEmitter', 'docforge.nav.MkDocsNavEmitter')>",
+        "docstring": "Emitter responsible for transforming a ResolvedNav into an MkDocs-compatible\nnavigation structure.",
+        "members": {
+          "emit": {
+            "name": "emit",
+            "kind": "function",
+            "path": "docforge.cli.mkdocs.logic.MkDocsNavEmitter.emit",
+            "signature": "<bound method Alias.signature of Alias('emit', 'docforge.nav.mkdocs.MkDocsNavEmitter.emit')>",
+            "docstring": "Generate a list of navigation entries for mkdocs.yml.\n\nArgs:\n    nav: The resolved navigation data.\n\nReturns:\n    A list of dictionary mappings representing the MkDocs navigation."
+          }
+        }
+      },
+      "generate_sources": {
+        "name": "generate_sources",
+        "kind": "function",
+        "path": "docforge.cli.mkdocs.logic.generate_sources",
+        "signature": "<bound method Function.signature of Function('generate_sources', 9, 18)>",
+        "docstring": "Generate Markdown source files for the specified module."
+      },
+      "generate_config": {
+        "name": "generate_config",
+        "kind": "function",
+        "path": "docforge.cli.mkdocs.logic.generate_config",
+        "signature": "<bound method Function.signature of Function('generate_config', 20, 47)>",
+        "docstring": "Generate an mkdocs.yml configuration file."
+      },
+      "build": {
+        "name": "build",
+        "kind": "function",
+        "path": "docforge.cli.mkdocs.logic.build",
+        "signature": "<bound method Function.signature of Function('build', 49, 59)>",
+        "docstring": "Build the documentation site using MkDocs."
+      },
+      "serve": {
+        "name": "serve",
+        "kind": "function",
+        "path": "docforge.cli.mkdocs.logic.serve",
+        "signature": "<bound method Function.signature of Function('serve', 61, 69)>",
+        "docstring": "Serve the documentation site with live-reload using MkDocs."
+      }
+    }
+  }
+}

mcp_docs/modules/docforge.json

@@ -85,119 +85,8 @@
         "kind": "module",
         "path": "docforge.main",
         "signature": "<bound method Alias.signature of Alias('main', 'docforge.cli.main')>",
-        "docstring": "Main entry point for the doc-forge CLI. This module defines the core command\ngroup and the 'tree', 'generate', 'build', and 'serve' commands.",
+        "docstring": "Main entry point for the doc-forge CLI.",
         "members": {
-          "Path": {
-            "name": "Path",
-            "kind": "alias",
-            "path": "docforge.main.Path",
-            "signature": "<bound method Alias.signature of Alias('Path', 'docforge.cli.main.Path')>",
-            "docstring": null
-          },
-          "Sequence": {
-            "name": "Sequence",
-            "kind": "alias",
-            "path": "docforge.main.Sequence",
-            "signature": "<bound method Alias.signature of Alias('Sequence', 'docforge.cli.main.Sequence')>",
-            "docstring": null
-          },
-          "Optional": {
-            "name": "Optional",
-            "kind": "alias",
-            "path": "docforge.main.Optional",
-            "signature": "<bound method Alias.signature of Alias('Optional', 'docforge.cli.main.Optional')>",
-            "docstring": null
-          },
-          "click": {
-            "name": "click",
-            "kind": "alias",
-            "path": "docforge.main.click",
-            "signature": "<bound method Alias.signature of Alias('click', 'docforge.cli.main.click')>",
-            "docstring": null
-          },
-          "GriffeLoader": {
-            "name": "GriffeLoader",
-            "kind": "class",
-            "path": "docforge.main.GriffeLoader",
-            "signature": "<bound method Alias.signature of Alias('GriffeLoader', 'docforge.cli.main.GriffeLoader')>",
-            "docstring": "Loads Python modules and extracts documentation using the Griffe introspection engine.",
-            "members": {
-              "load_project": {
-                "name": "load_project",
-                "kind": "function",
-                "path": "docforge.main.GriffeLoader.load_project",
-                "signature": "<bound method Alias.signature of Alias('load_project', 'docforge.loaders.griffe_loader.GriffeLoader.load_project')>",
-                "docstring": "Load multiple modules and combine them into a single Project models.\n\nArgs:\n    module_paths: A list of dotted paths to the modules to load.\n    project_name: Optional name for the project. Defaults to the first module name.\n    skip_import_errors: If True, modules that fail to import will be skipped.\n\nReturns:\n    A Project instance containing the loaded modules."
-              },
-              "load_module": {
-                "name": "load_module",
-                "kind": "function",
-                "path": "docforge.main.GriffeLoader.load_module",
-                "signature": "<bound method Alias.signature of Alias('load_module', 'docforge.loaders.griffe_loader.GriffeLoader.load_module')>",
-                "docstring": "Load a single module and convert its introspection data into the docforge models.\n\nArgs:\n    path: The dotted path of the module to load.\n\nReturns:\n    A Module instance."
-              }
-            }
-          },
-          "discover_module_paths": {
-            "name": "discover_module_paths",
-            "kind": "function",
-            "path": "docforge.main.discover_module_paths",
-            "signature": "<bound method Alias.signature of Alias('discover_module_paths', 'docforge.cli.main.discover_module_paths')>",
-            "docstring": "Discover all Python modules under a package via filesystem traversal.\n\nRules:\n- Directory with __init__.py is treated as a package.\n- Any .py file is treated as a module.\n- All paths are converted to dotted module paths.\n\nArgs:\n    module_name: The name of the package to discover.\n    project_root: The root directory of the project. Defaults to current working directory.\n\nReturns:\n    A sorted list of dotted module paths."
-          },
-          "MkDocsRenderer": {
-            "name": "MkDocsRenderer",
-            "kind": "class",
-            "path": "docforge.main.MkDocsRenderer",
-            "signature": "<bound method Alias.signature of Alias('MkDocsRenderer', 'docforge.cli.main.MkDocsRenderer')>",
-            "docstring": "Renderer that generates Markdown source files formatted for the MkDocs\n'mkdocstrings' plugin.",
-            "members": {
-              "name": {
-                "name": "name",
-                "kind": "attribute",
-                "path": "docforge.main.MkDocsRenderer.name",
-                "signature": "<bound method Alias.signature of Alias('name', 'docforge.renderers.mkdocs_renderer.MkDocsRenderer.name')>",
-                "docstring": null
-              },
-              "generate_sources": {
-                "name": "generate_sources",
-                "kind": "function",
-                "path": "docforge.main.MkDocsRenderer.generate_sources",
-                "signature": "<bound method Alias.signature of Alias('generate_sources', 'docforge.renderers.mkdocs_renderer.MkDocsRenderer.generate_sources')>",
-                "docstring": "Produce a set of Markdown files in the output directory based on the\nprovided Project models.\n\nArgs:\n    project: The project models to render.\n    out_dir: Target directory for documentation files."
-              }
-            }
-          },
-          "MCPRenderer": {
-            "name": "MCPRenderer",
-            "kind": "class",
-            "path": "docforge.main.MCPRenderer",
-            "signature": "<bound method Alias.signature of Alias('MCPRenderer', 'docforge.cli.main.MCPRenderer')>",
-            "docstring": "Renderer that emits MCP-native JSON resources from docforge models.",
-            "members": {
-              "name": {
-                "name": "name",
-                "kind": "attribute",
-                "path": "docforge.main.MCPRenderer.name",
-                "signature": "<bound method Alias.signature of Alias('name', 'docforge.renderers.mcp_renderer.MCPRenderer.name')>",
-                "docstring": null
-              },
-              "generate_sources": {
-                "name": "generate_sources",
-                "kind": "function",
-                "path": "docforge.main.MCPRenderer.generate_sources",
-                "signature": "<bound method Alias.signature of Alias('generate_sources', 'docforge.renderers.mcp_renderer.MCPRenderer.generate_sources')>",
-                "docstring": "Generate MCP-compatible JSON resources and navigation for the project."
-              }
-            }
-          },
-          "mkdocs_cmd": {
-            "name": "mkdocs_cmd",
-            "kind": "function",
-            "path": "docforge.main.mkdocs_cmd",
-            "signature": "<bound method Alias.signature of Alias('mkdocs_cmd', 'docforge.cli.main.mkdocs_cmd')>",
-            "docstring": "Generate an mkdocs.yml configuration file by combining a template with\nthe navigation structure resolved from a docforge.nav.yml file.\n\nArgs:\n    docs_dir: Path to the directory containing documentation Markdown files.\n    nav_file: Path to the docforge.nav.yml specification.\n    template: Optional path to an mkdocs.yml template.\n    out: Path where the final mkdocs.yml will be written.\n    site_name: The name of the documentation site."
-          },
           "cli": {
             "name": "cli",
             "kind": "function",
@@ -205,48 +94,6 @@
             "signature": "<bound method Alias.signature of Alias('cli', 'docforge.cli.main.cli')>",
             "docstring": "doc-forge CLI: A tool for introspecting Python projects and generating\ndocumentation."
           },
-          "tree": {
-            "name": "tree",
-            "kind": "function",
-            "path": "docforge.main.tree",
-            "signature": "<bound method Alias.signature of Alias('tree', 'docforge.cli.main.tree')>",
-            "docstring": "Visualize the project structure including modules and their members.\n\nArgs:\n    modules: List of module paths to introspect.\n    project_name: Optional project name override."
-          },
-          "generate": {
-            "name": "generate",
-            "kind": "function",
-            "path": "docforge.main.generate",
-            "signature": "<bound method Alias.signature of Alias('generate', 'docforge.cli.main.generate')>",
-            "docstring": "Generate Markdown source files for the specified module.\n\nArgs:\n    module: The primary module path to document.\n    project_name: Optional project name override.\n    docs_dir: Directory where documentation sources will be written."
-          },
-          "generate_mcp": {
-            "name": "generate_mcp",
-            "kind": "function",
-            "path": "docforge.main.generate_mcp",
-            "signature": "<bound method Alias.signature of Alias('generate_mcp', 'docforge.cli.main.generate_mcp')>",
-            "docstring": "Generate MCP-compatible documentation resources for the specified module.\n\nArgs:\n    module: The primary module path to document.\n    project_name: Optional project name override.\n    out_dir: Directory where MCP resources will be written."
-          },
-          "build": {
-            "name": "build",
-            "kind": "function",
-            "path": "docforge.main.build",
-            "signature": "<bound method Alias.signature of Alias('build', 'docforge.cli.main.build')>",
-            "docstring": "Build the documentation site using MkDocs.\n\nArgs:\n    mkdocs_yml: Path to the mkdocs.yml configuration file."
-          },
-          "serve_mcp": {
-            "name": "serve_mcp",
-            "kind": "function",
-            "path": "docforge.main.serve_mcp",
-            "signature": "<bound method Alias.signature of Alias('serve_mcp', 'docforge.cli.main.serve_mcp')>",
-            "docstring": "Serve MCP documentation from the local mcp_docs directory."
-          },
-          "serve": {
-            "name": "serve",
-            "kind": "function",
-            "path": "docforge.main.serve",
-            "signature": "<bound method Alias.signature of Alias('serve', 'docforge.cli.main.serve')>",
-            "docstring": "Serve the documentation site with live-reload using MkDocs.\n\nArgs:\n    mkdocs_yml: Path to the mkdocs.yml configuration file."
-          },
           "main": {
             "name": "main",
             "kind": "function",
@@ -268,54 +115,135 @@
             "kind": "module",
             "path": "docforge.cli.main",
             "signature": null,
-            "docstring": "Main entry point for the doc-forge CLI. This module defines the core command\ngroup and the 'tree', 'generate', 'build', and 'serve' commands.",
+            "docstring": "Main entry point for the doc-forge CLI.",
             "members": {
+              "cli": {
+                "name": "cli",
+                "kind": "function",
+                "path": "docforge.cli.main.cli",
+                "signature": "<bound method Alias.signature of Alias('cli', 'docforge.cli.commands.cli')>",
+                "docstring": "doc-forge CLI: A tool for introspecting Python projects and generating\ndocumentation."
+              },
+              "main": {
+                "name": "main",
+                "kind": "function",
+                "path": "docforge.cli.main.main",
+                "signature": "<bound method Function.signature of Function('main', 6, 10)>",
+                "docstring": "CLI Entry point. Boots the click application."
+              }
+            }
+          },
+          "commands": {
+            "name": "commands",
+            "kind": "module",
+            "path": "docforge.cli.commands",
+            "signature": null,
+            "docstring": null,
+            "members": {
+              "click": {
+                "name": "click",
+                "kind": "alias",
+                "path": "docforge.cli.commands.click",
+                "signature": "<bound method Alias.signature of Alias('click', 'click')>",
+                "docstring": null
+              },
               "Path": {
                 "name": "Path",
                 "kind": "alias",
-                "path": "docforge.cli.main.Path",
+                "path": "docforge.cli.commands.Path",
                 "signature": "<bound method Alias.signature of Alias('Path', 'pathlib.Path')>",
                 "docstring": null
               },
               "Sequence": {
                 "name": "Sequence",
                 "kind": "alias",
-                "path": "docforge.cli.main.Sequence",
+                "path": "docforge.cli.commands.Sequence",
                 "signature": "<bound method Alias.signature of Alias('Sequence', 'typing.Sequence')>",
                 "docstring": null
               },
               "Optional": {
                 "name": "Optional",
                 "kind": "alias",
-                "path": "docforge.cli.main.Optional",
+                "path": "docforge.cli.commands.Optional",
                 "signature": "<bound method Alias.signature of Alias('Optional', 'typing.Optional')>",
                 "docstring": null
               },
-              "click": {
-                "name": "click",
-                "kind": "alias",
-                "path": "docforge.cli.main.click",
-                "signature": "<bound method Alias.signature of Alias('click', 'click')>",
-                "docstring": null
-              },
               "GriffeLoader": {
                 "name": "GriffeLoader",
                 "kind": "class",
-                "path": "docforge.cli.main.GriffeLoader",
+                "path": "docforge.cli.commands.GriffeLoader",
                 "signature": "<bound method Alias.signature of Alias('GriffeLoader', 'docforge.loaders.GriffeLoader')>",
                 "docstring": "Loads Python modules and extracts documentation using the Griffe introspection engine.",
                 "members": {
                   "load_project": {
                     "name": "load_project",
                     "kind": "function",
-                    "path": "docforge.cli.main.GriffeLoader.load_project",
+                    "path": "docforge.cli.commands.GriffeLoader.load_project",
                     "signature": "<bound method Alias.signature of Alias('load_project', 'docforge.loaders.griffe_loader.GriffeLoader.load_project')>",
                     "docstring": "Load multiple modules and combine them into a single Project models.\n\nArgs:\n    module_paths: A list of dotted paths to the modules to load.\n    project_name: Optional name for the project. Defaults to the first module name.\n    skip_import_errors: If True, modules that fail to import will be skipped.\n\nReturns:\n    A Project instance containing the loaded modules."
                   },
                   "load_module": {
                     "name": "load_module",
                     "kind": "function",
-                    "path": "docforge.cli.main.GriffeLoader.load_module",
+                    "path": "docforge.cli.commands.GriffeLoader.load_module",
+                    "signature": "<bound method Alias.signature of Alias('load_module', 'docforge.loaders.griffe_loader.GriffeLoader.load_module')>",
+                    "docstring": "Load a single module and convert its introspection data into the docforge models.\n\nArgs:\n    path: The dotted path of the module to load.\n\nReturns:\n    A Module instance."
+                  }
+                }
+              },
+              "mkdocs_logic": {
+                "name": "mkdocs_logic",
+                "kind": "module",
+                "path": "docforge.cli.commands.mkdocs_logic",
+                "signature": "<bound method Alias.signature of Alias('mkdocs_logic', 'docforge.cli.mkdocs.logic')>",
+                "docstring": null,
+                "members": {
+                  "Path": {
+                    "name": "Path",
+                    "kind": "alias",
+                    "path": "docforge.cli.commands.mkdocs_logic.Path",
+                    "signature": "<bound method Alias.signature of Alias('Path', 'docforge.cli.mkdocs.logic.Path')>",
+                    "docstring": null
+                  },
+                  "resources": {
+                    "name": "resources",
+                    "kind": "alias",
+                    "path": "docforge.cli.commands.mkdocs_logic.resources",
+                    "signature": "<bound method Alias.signature of Alias('resources', 'docforge.cli.mkdocs.logic.resources')>",
+                    "docstring": null
+                  },
+                  "click": {
+                    "name": "click",
+                    "kind": "alias",
+                    "path": "docforge.cli.commands.mkdocs_logic.click",
+                    "signature": "<bound method Alias.signature of Alias('click', 'docforge.cli.mkdocs.logic.click')>",
+                    "docstring": null
+                  },
+                  "yaml": {
+                    "name": "yaml",
+                    "kind": "alias",
+                    "path": "docforge.cli.commands.mkdocs_logic.yaml",
+                    "signature": "<bound method Alias.signature of Alias('yaml', 'docforge.cli.mkdocs.logic.yaml')>",
+                    "docstring": null
+                  },
+                  "GriffeLoader": {
+                    "name": "GriffeLoader",
+                    "kind": "class",
+                    "path": "docforge.cli.commands.mkdocs_logic.GriffeLoader",
+                    "signature": "<bound method Alias.signature of Alias('GriffeLoader', 'docforge.cli.mkdocs.logic.GriffeLoader')>",
+                    "docstring": "Loads Python modules and extracts documentation using the Griffe introspection engine.",
+                    "members": {
+                      "load_project": {
+                        "name": "load_project",
+                        "kind": "function",
+                        "path": "docforge.cli.commands.mkdocs_logic.GriffeLoader.load_project",
+                        "signature": "<bound method Alias.signature of Alias('load_project', 'docforge.loaders.griffe_loader.GriffeLoader.load_project')>",
+                        "docstring": "Load multiple modules and combine them into a single Project models.\n\nArgs:\n    module_paths: A list of dotted paths to the modules to load.\n    project_name: Optional name for the project. Defaults to the first module name.\n    skip_import_errors: If True, modules that fail to import will be skipped.\n\nReturns:\n    A Project instance containing the loaded modules."
+                      },
+                      "load_module": {
+                        "name": "load_module",
+                        "kind": "function",
+                        "path": "docforge.cli.commands.mkdocs_logic.GriffeLoader.load_module",
                         "signature": "<bound method Alias.signature of Alias('load_module', 'docforge.loaders.griffe_loader.GriffeLoader.load_module')>",
                         "docstring": "Load a single module and convert its introspection data into the docforge models.\n\nArgs:\n    path: The dotted path of the module to load.\n\nReturns:\n    A Module instance."
                       }
@@ -324,118 +252,369 @@
                   "discover_module_paths": {
                     "name": "discover_module_paths",
                     "kind": "function",
-                "path": "docforge.cli.main.discover_module_paths",
-                "signature": "<bound method Alias.signature of Alias('discover_module_paths', 'docforge.loaders.discover_module_paths')>",
+                    "path": "docforge.cli.commands.mkdocs_logic.discover_module_paths",
+                    "signature": "<bound method Alias.signature of Alias('discover_module_paths', 'docforge.cli.mkdocs.logic.discover_module_paths')>",
                     "docstring": "Discover all Python modules under a package via filesystem traversal.\n\nRules:\n- Directory with __init__.py is treated as a package.\n- Any .py file is treated as a module.\n- All paths are converted to dotted module paths.\n\nArgs:\n    module_name: The name of the package to discover.\n    project_root: The root directory of the project. Defaults to current working directory.\n\nReturns:\n    A sorted list of dotted module paths."
                   },
                   "MkDocsRenderer": {
                     "name": "MkDocsRenderer",
                     "kind": "class",
-                "path": "docforge.cli.main.MkDocsRenderer",
-                "signature": "<bound method Alias.signature of Alias('MkDocsRenderer', 'docforge.renderers.MkDocsRenderer')>",
+                    "path": "docforge.cli.commands.mkdocs_logic.MkDocsRenderer",
+                    "signature": "<bound method Alias.signature of Alias('MkDocsRenderer', 'docforge.cli.mkdocs.logic.MkDocsRenderer')>",
                     "docstring": "Renderer that generates Markdown source files formatted for the MkDocs\n'mkdocstrings' plugin.",
                     "members": {
                       "name": {
                         "name": "name",
                         "kind": "attribute",
-                    "path": "docforge.cli.main.MkDocsRenderer.name",
+                        "path": "docforge.cli.commands.mkdocs_logic.MkDocsRenderer.name",
                         "signature": "<bound method Alias.signature of Alias('name', 'docforge.renderers.mkdocs_renderer.MkDocsRenderer.name')>",
                         "docstring": null
                       },
                       "generate_sources": {
                         "name": "generate_sources",
                         "kind": "function",
-                    "path": "docforge.cli.main.MkDocsRenderer.generate_sources",
+                        "path": "docforge.cli.commands.mkdocs_logic.MkDocsRenderer.generate_sources",
                         "signature": "<bound method Alias.signature of Alias('generate_sources', 'docforge.renderers.mkdocs_renderer.MkDocsRenderer.generate_sources')>",
                         "docstring": "Produce a set of Markdown files in the output directory based on the\nprovided Project models.\n\nArgs:\n    project: The project models to render.\n    out_dir: Target directory for documentation files."
                       }
                     }
                   },
+                  "load_nav_spec": {
+                    "name": "load_nav_spec",
+                    "kind": "function",
+                    "path": "docforge.cli.commands.mkdocs_logic.load_nav_spec",
+                    "signature": "<bound method Alias.signature of Alias('load_nav_spec', 'docforge.cli.mkdocs.logic.load_nav_spec')>",
+                    "docstring": "Utility function to load a NavSpec from a file.\n\nArgs:\n    path: Path to the navigation specification file.\n\nReturns:\n    A loaded NavSpec instance."
+                  },
+                  "resolve_nav": {
+                    "name": "resolve_nav",
+                    "kind": "function",
+                    "path": "docforge.cli.commands.mkdocs_logic.resolve_nav",
+                    "signature": "<bound method Alias.signature of Alias('resolve_nav', 'docforge.cli.mkdocs.logic.resolve_nav')>",
+                    "docstring": "Create a ResolvedNav by processing a NavSpec against the filesystem.\nThis expands globs and validates the existence of referenced files.\n\nArgs:\n    spec: The navigation specification to resolve.\n    docs_root: The root directory for documentation files.\n\nReturns:\n    A ResolvedNav instance.\n\nRaises:\n    FileNotFoundError: If a pattern doesn't match any files or the docs_root doesn't exist."
+                  },
+                  "MkDocsNavEmitter": {
+                    "name": "MkDocsNavEmitter",
+                    "kind": "class",
+                    "path": "docforge.cli.commands.mkdocs_logic.MkDocsNavEmitter",
+                    "signature": "<bound method Alias.signature of Alias('MkDocsNavEmitter', 'docforge.cli.mkdocs.logic.MkDocsNavEmitter')>",
+                    "docstring": "Emitter responsible for transforming a ResolvedNav into an MkDocs-compatible\nnavigation structure.",
+                    "members": {
+                      "emit": {
+                        "name": "emit",
+                        "kind": "function",
+                        "path": "docforge.cli.commands.mkdocs_logic.MkDocsNavEmitter.emit",
+                        "signature": "<bound method Alias.signature of Alias('emit', 'docforge.nav.mkdocs.MkDocsNavEmitter.emit')>",
+                        "docstring": "Generate a list of navigation entries for mkdocs.yml.\n\nArgs:\n    nav: The resolved navigation data.\n\nReturns:\n    A list of dictionary mappings representing the MkDocs navigation."
+                      }
+                    }
+                  },
+                  "generate_sources": {
+                    "name": "generate_sources",
+                    "kind": "function",
+                    "path": "docforge.cli.commands.mkdocs_logic.generate_sources",
+                    "signature": "<bound method Alias.signature of Alias('generate_sources', 'docforge.cli.mkdocs.logic.generate_sources')>",
+                    "docstring": "Generate Markdown source files for the specified module."
+                  },
+                  "generate_config": {
+                    "name": "generate_config",
+                    "kind": "function",
+                    "path": "docforge.cli.commands.mkdocs_logic.generate_config",
+                    "signature": "<bound method Alias.signature of Alias('generate_config', 'docforge.cli.mkdocs.logic.generate_config')>",
+                    "docstring": "Generate an mkdocs.yml configuration file."
+                  },
+                  "build": {
+                    "name": "build",
+                    "kind": "function",
+                    "path": "docforge.cli.commands.mkdocs_logic.build",
+                    "signature": "<bound method Alias.signature of Alias('build', 'docforge.cli.mkdocs.logic.build')>",
+                    "docstring": "Build the documentation site using MkDocs."
+                  },
+                  "serve": {
+                    "name": "serve",
+                    "kind": "function",
+                    "path": "docforge.cli.commands.mkdocs_logic.serve",
+                    "signature": "<bound method Alias.signature of Alias('serve', 'docforge.cli.mkdocs.logic.serve')>",
+                    "docstring": "Serve the documentation site with live-reload using MkDocs."
+                  }
+                }
+              },
+              "mcp_logic": {
+                "name": "mcp_logic",
+                "kind": "module",
+                "path": "docforge.cli.commands.mcp_logic",
+                "signature": "<bound method Alias.signature of Alias('mcp_logic', 'docforge.cli.mcp.logic')>",
+                "docstring": null,
+                "members": {
+                  "Path": {
+                    "name": "Path",
+                    "kind": "alias",
+                    "path": "docforge.cli.commands.mcp_logic.Path",
+                    "signature": "<bound method Alias.signature of Alias('Path', 'docforge.cli.mcp.logic.Path')>",
+                    "docstring": null
+                  },
+                  "click": {
+                    "name": "click",
+                    "kind": "alias",
+                    "path": "docforge.cli.commands.mcp_logic.click",
+                    "signature": "<bound method Alias.signature of Alias('click', 'docforge.cli.mcp.logic.click')>",
+                    "docstring": null
+                  },
+                  "GriffeLoader": {
+                    "name": "GriffeLoader",
+                    "kind": "class",
+                    "path": "docforge.cli.commands.mcp_logic.GriffeLoader",
+                    "signature": "<bound method Alias.signature of Alias('GriffeLoader', 'docforge.cli.mcp.logic.GriffeLoader')>",
+                    "docstring": "Loads Python modules and extracts documentation using the Griffe introspection engine.",
+                    "members": {
+                      "load_project": {
+                        "name": "load_project",
+                        "kind": "function",
+                        "path": "docforge.cli.commands.mcp_logic.GriffeLoader.load_project",
+                        "signature": "<bound method Alias.signature of Alias('load_project', 'docforge.loaders.griffe_loader.GriffeLoader.load_project')>",
+                        "docstring": "Load multiple modules and combine them into a single Project models.\n\nArgs:\n    module_paths: A list of dotted paths to the modules to load.\n    project_name: Optional name for the project. Defaults to the first module name.\n    skip_import_errors: If True, modules that fail to import will be skipped.\n\nReturns:\n    A Project instance containing the loaded modules."
+                      },
+                      "load_module": {
+                        "name": "load_module",
+                        "kind": "function",
+                        "path": "docforge.cli.commands.mcp_logic.GriffeLoader.load_module",
+                        "signature": "<bound method Alias.signature of Alias('load_module', 'docforge.loaders.griffe_loader.GriffeLoader.load_module')>",
+                        "docstring": "Load a single module and convert its introspection data into the docforge models.\n\nArgs:\n    path: The dotted path of the module to load.\n\nReturns:\n    A Module instance."
+                      }
+                    }
+                  },
+                  "discover_module_paths": {
+                    "name": "discover_module_paths",
+                    "kind": "function",
+                    "path": "docforge.cli.commands.mcp_logic.discover_module_paths",
+                    "signature": "<bound method Alias.signature of Alias('discover_module_paths', 'docforge.cli.mcp.logic.discover_module_paths')>",
+                    "docstring": "Discover all Python modules under a package via filesystem traversal.\n\nRules:\n- Directory with __init__.py is treated as a package.\n- Any .py file is treated as a module.\n- All paths are converted to dotted module paths.\n\nArgs:\n    module_name: The name of the package to discover.\n    project_root: The root directory of the project. Defaults to current working directory.\n\nReturns:\n    A sorted list of dotted module paths."
+                  },
                   "MCPRenderer": {
                     "name": "MCPRenderer",
                     "kind": "class",
-                "path": "docforge.cli.main.MCPRenderer",
-                "signature": "<bound method Alias.signature of Alias('MCPRenderer', 'docforge.renderers.MCPRenderer')>",
+                    "path": "docforge.cli.commands.mcp_logic.MCPRenderer",
+                    "signature": "<bound method Alias.signature of Alias('MCPRenderer', 'docforge.cli.mcp.logic.MCPRenderer')>",
                     "docstring": "Renderer that emits MCP-native JSON resources from docforge models.",
                     "members": {
                       "name": {
                         "name": "name",
                         "kind": "attribute",
-                    "path": "docforge.cli.main.MCPRenderer.name",
+                        "path": "docforge.cli.commands.mcp_logic.MCPRenderer.name",
                         "signature": "<bound method Alias.signature of Alias('name', 'docforge.renderers.mcp_renderer.MCPRenderer.name')>",
                         "docstring": null
                       },
                       "generate_sources": {
                         "name": "generate_sources",
                         "kind": "function",
-                    "path": "docforge.cli.main.MCPRenderer.generate_sources",
+                        "path": "docforge.cli.commands.mcp_logic.MCPRenderer.generate_sources",
                         "signature": "<bound method Alias.signature of Alias('generate_sources', 'docforge.renderers.mcp_renderer.MCPRenderer.generate_sources')>",
                         "docstring": "Generate MCP-compatible JSON resources and navigation for the project."
                       }
                     }
                   },
-              "mkdocs_cmd": {
-                "name": "mkdocs_cmd",
-                "kind": "function",
-                "path": "docforge.cli.main.mkdocs_cmd",
-                "signature": "<bound method Alias.signature of Alias('mkdocs_cmd', 'docforge.cli.mkdocs.mkdocs_cmd')>",
-                "docstring": "Generate an mkdocs.yml configuration file by combining a template with\nthe navigation structure resolved from a docforge.nav.yml file.\n\nArgs:\n    docs_dir: Path to the directory containing documentation Markdown files.\n    nav_file: Path to the docforge.nav.yml specification.\n    template: Optional path to an mkdocs.yml template.\n    out: Path where the final mkdocs.yml will be written.\n    site_name: The name of the documentation site."
+                  "MCPServer": {
+                    "name": "MCPServer",
+                    "kind": "class",
+                    "path": "docforge.cli.commands.mcp_logic.MCPServer",
+                    "signature": "<bound method Alias.signature of Alias('MCPServer', 'docforge.cli.mcp.logic.MCPServer')>",
+                    "docstring": "MCP server for serving a pre-built MCP documentation bundle.",
+                    "members": {
+                      "mcp_root": {
+                        "name": "mcp_root",
+                        "kind": "attribute",
+                        "path": "docforge.cli.commands.mcp_logic.MCPServer.mcp_root",
+                        "signature": "<bound method Alias.signature of Alias('mcp_root', 'docforge.servers.mcp_server.MCPServer.mcp_root')>",
+                        "docstring": null
                       },
-              "cli": {
-                "name": "cli",
-                "kind": "function",
-                "path": "docforge.cli.main.cli",
-                "signature": "<bound method Function.signature of Function('cli', 16, 22)>",
-                "docstring": "doc-forge CLI: A tool for introspecting Python projects and generating\ndocumentation."
+                      "app": {
+                        "name": "app",
+                        "kind": "attribute",
+                        "path": "docforge.cli.commands.mcp_logic.MCPServer.app",
+                        "signature": "<bound method Alias.signature of Alias('app', 'docforge.servers.mcp_server.MCPServer.app')>",
+                        "docstring": null
                       },
-              "tree": {
-                "name": "tree",
+                      "run": {
+                        "name": "run",
                         "kind": "function",
-                "path": "docforge.cli.main.tree",
-                "signature": "<bound method Function.signature of Function('tree', 31, 62)>",
-                "docstring": "Visualize the project structure including modules and their members.\n\nArgs:\n    modules: List of module paths to introspect.\n    project_name: Optional project name override."
+                        "path": "docforge.cli.commands.mcp_logic.MCPServer.run",
+                        "signature": "<bound method Alias.signature of Alias('run', 'docforge.servers.mcp_server.MCPServer.run')>",
+                        "docstring": "Start the MCP server.\n\nArgs:\n    transport: MCP transport (default: streamable-http)"
+                      }
+                    }
                   },
-              "generate": {
-                "name": "generate",
+                  "generate_resources": {
+                    "name": "generate_resources",
                     "kind": "function",
-                "path": "docforge.cli.main.generate",
-                "signature": "<bound method Function.signature of Function('generate', 82, 122)>",
-                "docstring": "Generate Markdown source files for the specified module.\n\nArgs:\n    module: The primary module path to document.\n    project_name: Optional project name override.\n    docs_dir: Directory where documentation sources will be written."
-              },
-              "generate_mcp": {
-                "name": "generate_mcp",
-                "kind": "function",
-                "path": "docforge.cli.main.generate_mcp",
-                "signature": "<bound method Function.signature of Function('generate_mcp', 129, 168)>",
-                "docstring": "Generate MCP-compatible documentation resources for the specified module.\n\nArgs:\n    module: The primary module path to document.\n    project_name: Optional project name override.\n    out_dir: Directory where MCP resources will be written."
-              },
-              "build": {
-                "name": "build",
-                "kind": "function",
-                "path": "docforge.cli.main.build",
-                "signature": "<bound method Function.signature of Function('build', 175, 196)>",
-                "docstring": "Build the documentation site using MkDocs.\n\nArgs:\n    mkdocs_yml: Path to the mkdocs.yml configuration file."
-              },
-              "serve_mcp": {
-                "name": "serve_mcp",
-                "kind": "function",
-                "path": "docforge.cli.main.serve_mcp",
-                "signature": "<bound method Function.signature of Function('serve_mcp', 203, 230)>",
-                "docstring": "Serve MCP documentation from the local mcp_docs directory."
+                    "path": "docforge.cli.commands.mcp_logic.generate_resources",
+                    "signature": "<bound method Alias.signature of Alias('generate_resources', 'docforge.cli.mcp.logic.generate_resources')>",
+                    "docstring": "Generate MCP-compatible documentation resources."
                   },
                   "serve": {
                     "name": "serve",
                     "kind": "function",
-                "path": "docforge.cli.main.serve",
-                "signature": "<bound method Function.signature of Function('serve', 237, 260)>",
-                "docstring": "Serve the documentation site with live-reload using MkDocs.\n\nArgs:\n    mkdocs_yml: Path to the mkdocs.yml configuration file."
+                    "path": "docforge.cli.commands.mcp_logic.serve",
+                    "signature": "<bound method Alias.signature of Alias('serve', 'docforge.cli.mcp.logic.serve')>",
+                    "docstring": "Serve MCP documentation."
+                  }
+                }
               },
-              "main": {
-                "name": "main",
+              "cli": {
+                "name": "cli",
                 "kind": "function",
-                "path": "docforge.cli.main.main",
-                "signature": "<bound method Function.signature of Function('main', 267, 271)>",
-                "docstring": "CLI Entry point. Boots the click application."
+                "path": "docforge.cli.commands.cli",
+                "signature": "<bound method Function.signature of Function('cli', 8, 14)>",
+                "docstring": "doc-forge CLI: A tool for introspecting Python projects and generating\ndocumentation."
+              },
+              "build": {
+                "name": "build",
+                "kind": "function",
+                "path": "docforge.cli.commands.build",
+                "signature": "<bound method Function.signature of Function('build', 16, 69)>",
+                "docstring": "Build documentation (MkDocs site or MCP resources)."
+              },
+              "serve": {
+                "name": "serve",
+                "kind": "function",
+                "path": "docforge.cli.commands.serve",
+                "signature": "<bound method Function.signature of Function('serve', 71, 93)>",
+                "docstring": "Serve documentation."
+              },
+              "tree": {
+                "name": "tree",
+                "kind": "function",
+                "path": "docforge.cli.commands.tree",
+                "signature": "<bound method Function.signature of Function('tree', 95, 121)>",
+                "docstring": "Visualize the project structure."
+              }
+            }
+          },
+          "mcp": {
+            "name": "mcp",
+            "kind": "module",
+            "path": "docforge.cli.mcp",
+            "signature": null,
+            "docstring": null,
+            "members": {
+              "logic": {
+                "name": "logic",
+                "kind": "module",
+                "path": "docforge.cli.mcp.logic",
+                "signature": null,
+                "docstring": null,
+                "members": {
+                  "Path": {
+                    "name": "Path",
+                    "kind": "alias",
+                    "path": "docforge.cli.mcp.logic.Path",
+                    "signature": "<bound method Alias.signature of Alias('Path', 'pathlib.Path')>",
+                    "docstring": null
+                  },
+                  "click": {
+                    "name": "click",
+                    "kind": "alias",
+                    "path": "docforge.cli.mcp.logic.click",
+                    "signature": "<bound method Alias.signature of Alias('click', 'click')>",
+                    "docstring": null
+                  },
+                  "GriffeLoader": {
+                    "name": "GriffeLoader",
+                    "kind": "class",
+                    "path": "docforge.cli.mcp.logic.GriffeLoader",
+                    "signature": "<bound method Alias.signature of Alias('GriffeLoader', 'docforge.loaders.GriffeLoader')>",
+                    "docstring": "Loads Python modules and extracts documentation using the Griffe introspection engine.",
+                    "members": {
+                      "load_project": {
+                        "name": "load_project",
+                        "kind": "function",
+                        "path": "docforge.cli.mcp.logic.GriffeLoader.load_project",
+                        "signature": "<bound method Alias.signature of Alias('load_project', 'docforge.loaders.griffe_loader.GriffeLoader.load_project')>",
+                        "docstring": "Load multiple modules and combine them into a single Project models.\n\nArgs:\n    module_paths: A list of dotted paths to the modules to load.\n    project_name: Optional name for the project. Defaults to the first module name.\n    skip_import_errors: If True, modules that fail to import will be skipped.\n\nReturns:\n    A Project instance containing the loaded modules."
+                      },
+                      "load_module": {
+                        "name": "load_module",
+                        "kind": "function",
+                        "path": "docforge.cli.mcp.logic.GriffeLoader.load_module",
+                        "signature": "<bound method Alias.signature of Alias('load_module', 'docforge.loaders.griffe_loader.GriffeLoader.load_module')>",
+                        "docstring": "Load a single module and convert its introspection data into the docforge models.\n\nArgs:\n    path: The dotted path of the module to load.\n\nReturns:\n    A Module instance."
+                      }
+                    }
+                  },
+                  "discover_module_paths": {
+                    "name": "discover_module_paths",
+                    "kind": "function",
+                    "path": "docforge.cli.mcp.logic.discover_module_paths",
+                    "signature": "<bound method Alias.signature of Alias('discover_module_paths', 'docforge.loaders.discover_module_paths')>",
+                    "docstring": "Discover all Python modules under a package via filesystem traversal.\n\nRules:\n- Directory with __init__.py is treated as a package.\n- Any .py file is treated as a module.\n- All paths are converted to dotted module paths.\n\nArgs:\n    module_name: The name of the package to discover.\n    project_root: The root directory of the project. Defaults to current working directory.\n\nReturns:\n    A sorted list of dotted module paths."
+                  },
+                  "MCPRenderer": {
+                    "name": "MCPRenderer",
+                    "kind": "class",
+                    "path": "docforge.cli.mcp.logic.MCPRenderer",
+                    "signature": "<bound method Alias.signature of Alias('MCPRenderer', 'docforge.renderers.MCPRenderer')>",
+                    "docstring": "Renderer that emits MCP-native JSON resources from docforge models.",
+                    "members": {
+                      "name": {
+                        "name": "name",
+                        "kind": "attribute",
+                        "path": "docforge.cli.mcp.logic.MCPRenderer.name",
+                        "signature": "<bound method Alias.signature of Alias('name', 'docforge.renderers.mcp_renderer.MCPRenderer.name')>",
+                        "docstring": null
+                      },
+                      "generate_sources": {
+                        "name": "generate_sources",
+                        "kind": "function",
+                        "path": "docforge.cli.mcp.logic.MCPRenderer.generate_sources",
+                        "signature": "<bound method Alias.signature of Alias('generate_sources', 'docforge.renderers.mcp_renderer.MCPRenderer.generate_sources')>",
+                        "docstring": "Generate MCP-compatible JSON resources and navigation for the project."
+                      }
+                    }
+                  },
+                  "MCPServer": {
+                    "name": "MCPServer",
+                    "kind": "class",
+                    "path": "docforge.cli.mcp.logic.MCPServer",
+                    "signature": "<bound method Alias.signature of Alias('MCPServer', 'docforge.servers.MCPServer')>",
+                    "docstring": "MCP server for serving a pre-built MCP documentation bundle.",
+                    "members": {
+                      "mcp_root": {
+                        "name": "mcp_root",
+                        "kind": "attribute",
+                        "path": "docforge.cli.mcp.logic.MCPServer.mcp_root",
+                        "signature": "<bound method Alias.signature of Alias('mcp_root', 'docforge.servers.mcp_server.MCPServer.mcp_root')>",
+                        "docstring": null
+                      },
+                      "app": {
+                        "name": "app",
+                        "kind": "attribute",
+                        "path": "docforge.cli.mcp.logic.MCPServer.app",
+                        "signature": "<bound method Alias.signature of Alias('app', 'docforge.servers.mcp_server.MCPServer.app')>",
+                        "docstring": null
+                      },
+                      "run": {
+                        "name": "run",
+                        "kind": "function",
+                        "path": "docforge.cli.mcp.logic.MCPServer.run",
+                        "signature": "<bound method Alias.signature of Alias('run', 'docforge.servers.mcp_server.MCPServer.run')>",
+                        "docstring": "Start the MCP server.\n\nArgs:\n    transport: MCP transport (default: streamable-http)"
+                      }
+                    }
+                  },
+                  "generate_resources": {
+                    "name": "generate_resources",
+                    "kind": "function",
+                    "path": "docforge.cli.mcp.logic.generate_resources",
+                    "signature": "<bound method Function.signature of Function('generate_resources', 7, 16)>",
+                    "docstring": "Generate MCP-compatible documentation resources."
+                  },
+                  "serve": {
+                    "name": "serve",
+                    "kind": "function",
+                    "path": "docforge.cli.mcp.logic.serve",
+                    "signature": "<bound method Function.signature of Function('serve', 18, 39)>",
+                    "docstring": "Serve MCP documentation."
+                  }
+                }
               }
             }
           },
@@ -444,93 +623,155 @@
             "kind": "module",
             "path": "docforge.cli.mkdocs",
             "signature": null,
-            "docstring": "This module contains the 'mkdocs' CLI command, which orchestrates the generation\nof the main mkdocs.yml configuration file.",
+            "docstring": null,
+            "members": {
+              "logic": {
+                "name": "logic",
+                "kind": "module",
+                "path": "docforge.cli.mkdocs.logic",
+                "signature": null,
+                "docstring": null,
                 "members": {
                   "Path": {
                     "name": "Path",
                     "kind": "alias",
-                "path": "docforge.cli.mkdocs.Path",
+                    "path": "docforge.cli.mkdocs.logic.Path",
                     "signature": "<bound method Alias.signature of Alias('Path', 'pathlib.Path')>",
                     "docstring": null
                   },
                   "resources": {
                     "name": "resources",
                     "kind": "alias",
-                "path": "docforge.cli.mkdocs.resources",
+                    "path": "docforge.cli.mkdocs.logic.resources",
                     "signature": "<bound method Alias.signature of Alias('resources', 'importlib.resources')>",
                     "docstring": null
                   },
                   "click": {
                     "name": "click",
                     "kind": "alias",
-                "path": "docforge.cli.mkdocs.click",
+                    "path": "docforge.cli.mkdocs.logic.click",
                     "signature": "<bound method Alias.signature of Alias('click', 'click')>",
                     "docstring": null
                   },
                   "yaml": {
                     "name": "yaml",
                     "kind": "alias",
-                "path": "docforge.cli.mkdocs.yaml",
+                    "path": "docforge.cli.mkdocs.logic.yaml",
                     "signature": "<bound method Alias.signature of Alias('yaml', 'yaml')>",
                     "docstring": null
                   },
+                  "GriffeLoader": {
+                    "name": "GriffeLoader",
+                    "kind": "class",
+                    "path": "docforge.cli.mkdocs.logic.GriffeLoader",
+                    "signature": "<bound method Alias.signature of Alias('GriffeLoader', 'docforge.loaders.GriffeLoader')>",
+                    "docstring": "Loads Python modules and extracts documentation using the Griffe introspection engine.",
+                    "members": {
+                      "load_project": {
+                        "name": "load_project",
+                        "kind": "function",
+                        "path": "docforge.cli.mkdocs.logic.GriffeLoader.load_project",
+                        "signature": "<bound method Alias.signature of Alias('load_project', 'docforge.loaders.griffe_loader.GriffeLoader.load_project')>",
+                        "docstring": "Load multiple modules and combine them into a single Project models.\n\nArgs:\n    module_paths: A list of dotted paths to the modules to load.\n    project_name: Optional name for the project. Defaults to the first module name.\n    skip_import_errors: If True, modules that fail to import will be skipped.\n\nReturns:\n    A Project instance containing the loaded modules."
+                      },
+                      "load_module": {
+                        "name": "load_module",
+                        "kind": "function",
+                        "path": "docforge.cli.mkdocs.logic.GriffeLoader.load_module",
+                        "signature": "<bound method Alias.signature of Alias('load_module', 'docforge.loaders.griffe_loader.GriffeLoader.load_module')>",
+                        "docstring": "Load a single module and convert its introspection data into the docforge models.\n\nArgs:\n    path: The dotted path of the module to load.\n\nReturns:\n    A Module instance."
+                      }
+                    }
+                  },
+                  "discover_module_paths": {
+                    "name": "discover_module_paths",
+                    "kind": "function",
+                    "path": "docforge.cli.mkdocs.logic.discover_module_paths",
+                    "signature": "<bound method Alias.signature of Alias('discover_module_paths', 'docforge.loaders.discover_module_paths')>",
+                    "docstring": "Discover all Python modules under a package via filesystem traversal.\n\nRules:\n- Directory with __init__.py is treated as a package.\n- Any .py file is treated as a module.\n- All paths are converted to dotted module paths.\n\nArgs:\n    module_name: The name of the package to discover.\n    project_root: The root directory of the project. Defaults to current working directory.\n\nReturns:\n    A sorted list of dotted module paths."
+                  },
+                  "MkDocsRenderer": {
+                    "name": "MkDocsRenderer",
+                    "kind": "class",
+                    "path": "docforge.cli.mkdocs.logic.MkDocsRenderer",
+                    "signature": "<bound method Alias.signature of Alias('MkDocsRenderer', 'docforge.renderers.MkDocsRenderer')>",
+                    "docstring": "Renderer that generates Markdown source files formatted for the MkDocs\n'mkdocstrings' plugin.",
+                    "members": {
+                      "name": {
+                        "name": "name",
+                        "kind": "attribute",
+                        "path": "docforge.cli.mkdocs.logic.MkDocsRenderer.name",
+                        "signature": "<bound method Alias.signature of Alias('name', 'docforge.renderers.mkdocs_renderer.MkDocsRenderer.name')>",
+                        "docstring": null
+                      },
+                      "generate_sources": {
+                        "name": "generate_sources",
+                        "kind": "function",
+                        "path": "docforge.cli.mkdocs.logic.MkDocsRenderer.generate_sources",
+                        "signature": "<bound method Alias.signature of Alias('generate_sources', 'docforge.renderers.mkdocs_renderer.MkDocsRenderer.generate_sources')>",
+                        "docstring": "Produce a set of Markdown files in the output directory based on the\nprovided Project models.\n\nArgs:\n    project: The project models to render.\n    out_dir: Target directory for documentation files."
+                      }
+                    }
+                  },
                   "load_nav_spec": {
                     "name": "load_nav_spec",
                     "kind": "function",
-                "path": "docforge.cli.mkdocs.load_nav_spec",
+                    "path": "docforge.cli.mkdocs.logic.load_nav_spec",
                     "signature": "<bound method Alias.signature of Alias('load_nav_spec', 'docforge.nav.load_nav_spec')>",
                     "docstring": "Utility function to load a NavSpec from a file.\n\nArgs:\n    path: Path to the navigation specification file.\n\nReturns:\n    A loaded NavSpec instance."
                   },
                   "resolve_nav": {
                     "name": "resolve_nav",
                     "kind": "function",
-                "path": "docforge.cli.mkdocs.resolve_nav",
+                    "path": "docforge.cli.mkdocs.logic.resolve_nav",
                     "signature": "<bound method Alias.signature of Alias('resolve_nav', 'docforge.nav.resolve_nav')>",
                     "docstring": "Create a ResolvedNav by processing a NavSpec against the filesystem.\nThis expands globs and validates the existence of referenced files.\n\nArgs:\n    spec: The navigation specification to resolve.\n    docs_root: The root directory for documentation files.\n\nReturns:\n    A ResolvedNav instance.\n\nRaises:\n    FileNotFoundError: If a pattern doesn't match any files or the docs_root doesn't exist."
                   },
                   "MkDocsNavEmitter": {
                     "name": "MkDocsNavEmitter",
                     "kind": "class",
-                "path": "docforge.cli.mkdocs.MkDocsNavEmitter",
+                    "path": "docforge.cli.mkdocs.logic.MkDocsNavEmitter",
                     "signature": "<bound method Alias.signature of Alias('MkDocsNavEmitter', 'docforge.nav.MkDocsNavEmitter')>",
                     "docstring": "Emitter responsible for transforming a ResolvedNav into an MkDocs-compatible\nnavigation structure.",
                     "members": {
                       "emit": {
                         "name": "emit",
                         "kind": "function",
-                    "path": "docforge.cli.mkdocs.MkDocsNavEmitter.emit",
+                        "path": "docforge.cli.mkdocs.logic.MkDocsNavEmitter.emit",
                         "signature": "<bound method Alias.signature of Alias('emit', 'docforge.nav.mkdocs.MkDocsNavEmitter.emit')>",
                         "docstring": "Generate a list of navigation entries for mkdocs.yml.\n\nArgs:\n    nav: The resolved navigation data.\n\nReturns:\n    A list of dictionary mappings representing the MkDocs navigation."
                       }
                     }
                   },
-              "mkdocs_cmd": {
-                "name": "mkdocs_cmd",
+                  "generate_sources": {
+                    "name": "generate_sources",
                     "kind": "function",
-                "path": "docforge.cli.mkdocs.mkdocs_cmd",
-                "signature": "<bound method Function.signature of Function('mkdocs_cmd', 42, 116)>",
-                "docstring": "Generate an mkdocs.yml configuration file by combining a template with\nthe navigation structure resolved from a docforge.nav.yml file.\n\nArgs:\n    docs_dir: Path to the directory containing documentation Markdown files.\n    nav_file: Path to the docforge.nav.yml specification.\n    template: Optional path to an mkdocs.yml template.\n    out: Path where the final mkdocs.yml will be written.\n    site_name: The name of the documentation site."
+                    "path": "docforge.cli.mkdocs.logic.generate_sources",
+                    "signature": "<bound method Function.signature of Function('generate_sources', 9, 18)>",
+                    "docstring": "Generate Markdown source files for the specified module."
                   },
-              "Any": {
-                "name": "Any",
-                "kind": "alias",
-                "path": "docforge.cli.mkdocs.Any",
-                "signature": "<bound method Alias.signature of Alias('Any', 'typing.Any')>",
-                "docstring": null
+                  "generate_config": {
+                    "name": "generate_config",
+                    "kind": "function",
+                    "path": "docforge.cli.mkdocs.logic.generate_config",
+                    "signature": "<bound method Function.signature of Function('generate_config', 20, 47)>",
+                    "docstring": "Generate an mkdocs.yml configuration file."
                   },
-              "Dict": {
-                "name": "Dict",
-                "kind": "alias",
-                "path": "docforge.cli.mkdocs.Dict",
-                "signature": "<bound method Alias.signature of Alias('Dict', 'typing.Dict')>",
-                "docstring": null
+                  "build": {
+                    "name": "build",
+                    "kind": "function",
+                    "path": "docforge.cli.mkdocs.logic.build",
+                    "signature": "<bound method Function.signature of Function('build', 49, 59)>",
+                    "docstring": "Build the documentation site using MkDocs."
                   },
-              "Optional": {
-                "name": "Optional",
-                "kind": "alias",
-                "path": "docforge.cli.mkdocs.Optional",
-                "signature": "<bound method Alias.signature of Alias('Optional', 'typing.Optional')>",
-                "docstring": null
+                  "serve": {
+                    "name": "serve",
+                    "kind": "function",
+                    "path": "docforge.cli.mkdocs.logic.serve",
+                    "signature": "<bound method Function.signature of Function('serve', 61, 69)>",
+                    "docstring": "Serve the documentation site with live-reload using MkDocs."
+                  }
+                }
               }
             }
           }

mcp_docs/nav.json

@@ -7,14 +7,30 @@
     "module": "docforge.cli",
     "resource": "doc://modules/docforge.cli"
   },
+  {
+    "module": "docforge.cli.commands",
+    "resource": "doc://modules/docforge.cli.commands"
+  },
   {
     "module": "docforge.cli.main",
     "resource": "doc://modules/docforge.cli.main"
   },
+  {
+    "module": "docforge.cli.mcp",
+    "resource": "doc://modules/docforge.cli.mcp"
+  },
+  {
+    "module": "docforge.cli.mcp.logic",
+    "resource": "doc://modules/docforge.cli.mcp.logic"
+  },
   {
     "module": "docforge.cli.mkdocs",
     "resource": "doc://modules/docforge.cli.mkdocs"
   },
+  {
+    "module": "docforge.cli.mkdocs.logic",
+    "resource": "doc://modules/docforge.cli.mkdocs.logic"
+  },
   {
     "module": "docforge.loaders",
     "resource": "doc://modules/docforge.loaders"

mkdocs.yml

@@ -1,4 +1,4 @@
-site_name: DocForge
+site_name: docforge
 
 theme:
   name: material
@@ -57,4 +57,8 @@ nav:
 - CLI:
   - docforge/cli/index.md
   - docforge/cli/main.md
-  - docforge/cli/mkdocs.md
+  - docforge/cli/commands.md
+  - docforge/cli/mcp/index.md
+  - docforge/cli/mcp/logic.md
+  - docforge/cli/mkdocs/index.md
+  - docforge/cli/mkdocs/logic.md

tests/cli/conftest.py

@@ -1,111 +0,0 @@
-import json
-import pytest
-from pathlib import Path
-
-from click.testing import CliRunner
-
-
-@pytest.fixture
-def cli_runner() -> CliRunner:
-    """Click CLI runner."""
-    return CliRunner()
-
-
-@pytest.fixture
-def fake_mkdocs_yml(tmp_path: Path) -> Path:
-    """Create a minimal mkdocs.yml file."""
-    yml = tmp_path / "mkdocs.yml"
-    yml.write_text(
-        """
-site_name: Test Docs
-nav: []
-plugins:
-  - mkdocstrings
-""",
-        encoding="utf-8",
-    )
-    return yml
-
-
-@pytest.fixture
-def mock_mkdocs_load_config(monkeypatch):
-    """Mock mkdocs.config.load_config."""
-    def fake_load_config(path):
-        return object()  # dummy config object
-
-    monkeypatch.setattr(
-        "mkdocs.config.load_config",
-        fake_load_config,
-    )
-
-
-@pytest.fixture
-def mock_mkdocs_build(monkeypatch):
-    called = {"value": False}
-
-    def fake_build(config):
-        called["value"] = True
-
-    monkeypatch.setattr(
-        "mkdocs.commands.build.build",
-        fake_build,
-    )
-    return lambda: called["value"]
-
-
-@pytest.fixture
-def mock_mkdocs_serve(monkeypatch):
-    called = {"value": False}
-
-    def fake_serve(*args, **kwargs):
-        called["value"] = True
-
-    monkeypatch.setattr(
-        "mkdocs.commands.serve.serve",
-        fake_serve,
-    )
-    return lambda: called["value"]
-
-@pytest.fixture
-def fake_mcp_docs(tmp_path: Path) -> Path:
-    """
-    Create a minimal valid MCP bundle in mcp_docs/.
-    """
-    mcp_root = tmp_path / "mcp_docs"
-    modules_dir = mcp_root / "modules"
-    modules_dir.mkdir(parents=True)
-
-    (mcp_root / "index.json").write_text(
-        json.dumps({"project": "test", "type": "docforge-model"}),
-        encoding="utf-8",
-    )
-
-    (mcp_root / "nav.json").write_text(
-        json.dumps([]),
-        encoding="utf-8",
-    )
-
-    (modules_dir / "test.mod.json").write_text(
-        json.dumps({"module": "test.mod", "content": {}}),
-        encoding="utf-8",
-    )
-
-    return mcp_root
-
-
-@pytest.fixture
-def mock_mcp_server_run(monkeypatch):
-    """
-    Mock MCPServer.run so no real server is started.
-    """
-    called = {"value": False}
-
-    def fake_run(self, transport="streamable-http"):
-        called["value"] = True
-
-    monkeypatch.setattr(
-        "docforge.servers.MCPServer.run",
-        fake_run,
-    )
-
-    return lambda: called["value"]

tests/cli/test_build.py

@@ -1,20 +0,0 @@
-from docforge.cli.main import cli
-
-
-def test_build_command(
-    cli_runner,
-    fake_mkdocs_yml,
-    mock_mkdocs_load_config,
-    mock_mkdocs_build,
-):
-    result = cli_runner.invoke(
-        cli,
-        [
-            "build",
-            "--mkdocs-yml",
-            str(fake_mkdocs_yml),
-        ],
-    )
-
-    assert result.exit_code == 0
-    assert mock_mkdocs_build() is True

tests/cli/test_build_mcp.py

@@ -1,35 +1,29 @@
 from pathlib import Path
-
 from docforge.cli.main import cli
 
-
-def test_generate_command(cli_runner):
+def test_mcp_build(cli_runner):
     with cli_runner.isolated_filesystem():
         cwd = Path.cwd()
-
-        # Create package structure
         pkg = cwd / "testpkg"
         pkg.mkdir()
         (pkg / "__init__.py").write_text("")
         (pkg / "mod.py").write_text("def f(): ...\n")
 
-        docs_dir = cwd / "docs"
+        out_dir = cwd / "mcp_docs"
 
         result = cli_runner.invoke(
             cli,
             [
-                "generate",
+                "build",
+                "--mcp",
                 "--module",
                 "testpkg",
-                "--docs-dir",
-                str(docs_dir),
+                "--out-dir",
+                str(out_dir),
             ],
         )
 
         assert result.exit_code == 0
-
-        md = docs_dir / "testpkg" / "mod.md"
-        assert md.exists()
-
-        content = md.read_text()
-        assert "::: testpkg.mod" in content
+        assert (out_dir / "index.json").exists()
+        assert (out_dir / "nav.json").exists()
+        assert (out_dir / "modules" / "testpkg.mod.json").exists()

tests/cli/test_build_mkdocs.py

@@ -0,0 +1,99 @@
+from pathlib import Path
+from docforge.cli.main import cli
+
+def test_mkdocs_build_full_flow(
+    cli_runner,
+    mock_mkdocs_build,
+    mock_mkdocs_load_config,
+    tmp_path,
+):
+    # This test covers what used to be generate + mkdocs + build
+    with cli_runner.isolated_filesystem():
+        cwd = Path.cwd()
+        pkg = cwd / "testpkg"
+        pkg.mkdir()
+        (pkg / "__init__.py").write_text("")
+        (pkg / "mod.py").write_text("def f(): ...\n")
+
+        nav_file = cwd / "docforge.nav.yml"
+        nav_file.write_text("home: testpkg/index.md\ngroups: {}\n")
+        
+        # We need to create a dummy testpkg/index.md for nav resolution if it's there
+        # But generate_sources will create it. 
+        # Wait, the current logic runs generate_sources first, THEN generate_config.
+        
+        result = cli_runner.invoke(
+            cli,
+            [
+                "build",
+                "--mkdocs",
+                "--module",
+                "testpkg",
+                "--site-name",
+                "Test Site",
+                "--docs-dir",
+                "docs",
+                "--mkdocs-yml",
+                "mkdocs.yml",
+            ],
+        )
+
+        assert result.exit_code == 0
+        assert mock_mkdocs_build() is True
+        assert (cwd / "mkdocs.yml").exists()
+        assert (cwd / "docs" / "testpkg" / "mod.md").exists()
+
+def test_mkdocs_build_missing_module_fails(cli_runner):
+    result = cli_runner.invoke(cli, ["build", "--mkdocs", "--site-name", "Test"])
+    assert result.exit_code != 0
+    assert "--module is required" in result.output
+
+def test_mkdocs_build_without_site_name_uses_module_as_default_full_flow(
+    cli_runner,
+    mock_mkdocs_build,
+    mock_mkdocs_load_config,
+):
+    # Full integration test: real generation, real config, mocked mkdocs build
+    with cli_runner.isolated_filesystem():
+        cwd = Path.cwd()
+
+        # Create a minimal Python package
+        pkg = cwd / "testpkg"
+        pkg.mkdir()
+        (pkg / "__init__.py").write_text("")
+        (pkg / "mod.py").write_text("def f(): ...\n")
+
+        # Create nav spec expected by generate_config
+        nav_file = cwd / "docforge.nav.yml"
+        nav_file.write_text(
+            "home: testpkg/index.md\ngroups: {}\n",
+            encoding="utf-8",
+        )
+
+        result = cli_runner.invoke(
+            cli,
+            [
+                "build",
+                "--mkdocs",
+                "--module",
+                "testpkg",
+                "--docs-dir",
+                "docs",
+                "--mkdocs-yml",
+                "mkdocs.yml",
+            ],
+        )
+
+        assert result.exit_code == 0
+        assert mock_mkdocs_build() is True
+
+        # MkDocs config must exist
+        mkdocs_yml = cwd / "mkdocs.yml"
+        assert mkdocs_yml.exists()
+
+        # Site name must default to module name
+        content = mkdocs_yml.read_text()
+        assert "site_name: testpkg" in content
+
+        # Docs must be generated
+        assert (cwd / "docs" / "testpkg" / "mod.md").exists()

tests/cli/test_mkdocs.py

@@ -1,123 +0,0 @@
-from pathlib import Path
-
-import yaml
-from click.testing import CliRunner
-
-from docforge.cli.main import cli
-
-
-def _write_nav_spec(path: Path) -> None:
-    path.write_text(
-        """
-home: openapi_first/index.md
-groups:
-  Core:
-    - openapi_first/app.md
-    - openapi_first/client.md
-""".strip(),
-        encoding="utf-8",
-    )
-
-
-def _write_docs(docs: Path) -> None:
-    files = [
-        "openapi_first/index.md",
-        "openapi_first/app.md",
-        "openapi_first/client.md",
-    ]
-    for rel in files:
-        p = docs / rel
-        p.parent.mkdir(parents=True, exist_ok=True)
-        p.write_text(f"# {rel}", encoding="utf-8")
-
-
-def test_mkdocs_uses_builtin_template(tmp_path: Path) -> None:
-    docs = tmp_path / "docs"
-    docs.mkdir()
-
-    nav_file = tmp_path / "docforge.nav.yml"
-    out_file = tmp_path / "mkdocs.yml"
-
-    _write_docs(docs)
-    _write_nav_spec(nav_file)
-
-    runner = CliRunner()
-    result = runner.invoke(
-        cli,
-        [
-            "mkdocs",
-            "--site-name",
-            "DocForge",
-            "--docs-dir",
-            str(docs),
-            "--nav",
-            str(nav_file),
-            "--out",
-            str(out_file),
-        ],
-    )
-
-    assert result.exit_code == 0
-    assert out_file.exists()
-
-
-def test_mkdocs_overrides_template(tmp_path: Path) -> None:
-    docs = tmp_path / "docs"
-    docs.mkdir()
-
-    nav_file = tmp_path / "docforge.nav.yml"
-    template = tmp_path / "custom.yml"
-    out_file = tmp_path / "mkdocs.yml"
-
-    _write_docs(docs)
-    _write_nav_spec(nav_file)
-
-    template.write_text(
-        """
-site_name: Custom Site
-theme:
-  name: readthedocs
-""".strip(),
-        encoding="utf-8",
-    )
-
-    runner = CliRunner()
-    result = runner.invoke(
-        cli,
-        [
-            "mkdocs",
-            "--site-name",
-            "Override Site",
-            "--docs-dir",
-            str(docs),
-            "--nav",
-            str(nav_file),
-            "--template",
-            str(template),
-            "--out",
-            str(out_file),
-        ],
-    )
-
-    assert result.exit_code == 0
-    assert out_file.exists()
-
-
-def test_mkdocs_missing_nav_fails(tmp_path: Path) -> None:
-    docs = tmp_path / "docs"
-    docs.mkdir()
-
-    runner = CliRunner()
-    result = runner.invoke(
-        cli,
-        [
-            "mkdocs",
-            "--site-name",
-            "DocForge",
-            "--docs-dir",
-            str(docs),
-        ],
-    )
-
-    assert result.exit_code != 0
-    assert "Nav spec not found" in result.output

tests/cli/test_serve_mcp.py

@@ -1,7 +1,6 @@
 from docforge.cli.main import cli
 
-
-def test_serve_mcp(
+def test_mcp_serve(
     cli_runner,
     fake_mcp_docs,
     mock_mcp_server_run,
@@ -11,7 +10,7 @@ def test_serve_mcp(
 
     result = cli_runner.invoke(
         cli,
-        ["serve-mcp"],
+        ["serve", "--mcp", "--out-dir", str(fake_mcp_docs)],
     )
 
     assert result.exit_code == 0

tests/cli/test_serve_mkdocs.py

@@ -1,7 +1,6 @@
 from docforge.cli.main import cli
 
-
-def test_serve_command(
+def test_mkdocs_serve(
     cli_runner,
     fake_mkdocs_yml,
     mock_mkdocs_serve,
@@ -10,6 +9,7 @@ def test_serve_command(
         cli,
         [
             "serve",
+            "--mkdocs",
             "--mkdocs-yml",
             str(fake_mkdocs_yml),
         ],

tests/cli/test_tree.py

@@ -1,24 +0,0 @@
-from docforge.cli.main import cli
-
-
-def test_tree_command(cli_runner, temp_package):
-    (temp_package / "mod.py").write_text(
-        '''
-class A:
-    def f(self): ...
-'''
-    )
-
-    result = cli_runner.invoke(
-        cli,
-        [
-            "tree",
-            "--modules",
-            "testpkg.mod",
-        ],
-    )
-
-    assert result.exit_code == 0
-    assert "testpkg" in result.output
-    assert "mod" in result.output
-    assert "A" in result.output

tests/conftest.py

@@ -1,7 +1,9 @@
 import sys
+import json
+import pytest
 from pathlib import Path
 
-import pytest
+from click.testing import CliRunner
 
 
 @pytest.fixture
@@ -16,3 +18,109 @@ def temp_package(tmp_path: Path):
     sys.path.insert(0, str(tmp_path))
     yield pkg
     sys.path.remove(str(tmp_path))
+
+
+@pytest.fixture
+def cli_runner() -> CliRunner:
+    """Click CLI runner."""
+    return CliRunner()
+
+
+@pytest.fixture
+def fake_mkdocs_yml(tmp_path: Path) -> Path:
+    """Create a minimal mkdocs.yml file."""
+    yml = tmp_path / "mkdocs.yml"
+    yml.write_text(
+        """
+site_name: Test Docs
+nav: []
+plugins:
+  - mkdocstrings
+""",
+        encoding="utf-8",
+    )
+    return yml
+
+
+@pytest.fixture
+def mock_mkdocs_load_config(monkeypatch):
+    """Mock mkdocs.config.load_config."""
+    def fake_load_config(path):
+        return object()  # dummy config object
+
+    monkeypatch.setattr(
+        "mkdocs.config.load_config",
+        fake_load_config,
+    )
+
+
+@pytest.fixture
+def mock_mkdocs_build(monkeypatch):
+    called = {"value": False}
+
+    def fake_build(config):
+        called["value"] = True
+
+    monkeypatch.setattr(
+        "mkdocs.commands.build.build",
+        fake_build,
+    )
+    return lambda: called["value"]
+
+
+@pytest.fixture
+def mock_mkdocs_serve(monkeypatch):
+    called = {"value": False}
+
+    def fake_serve(*args, **kwargs):
+        called["value"] = True
+
+    monkeypatch.setattr(
+        "mkdocs.commands.serve.serve",
+        fake_serve,
+    )
+    return lambda: called["value"]
+
+@pytest.fixture
+def fake_mcp_docs(tmp_path: Path) -> Path:
+    """
+    Create a minimal valid MCP bundle in mcp_docs/.
+    """
+    mcp_root = tmp_path / "mcp_docs"
+    modules_dir = mcp_root / "modules"
+    modules_dir.mkdir(parents=True)
+
+    (mcp_root / "index.json").write_text(
+        json.dumps({"project": "test", "type": "docforge-model"}),
+        encoding="utf-8",
+    )
+
+    (mcp_root / "nav.json").write_text(
+        json.dumps([]),
+        encoding="utf-8",
+    )
+
+    (modules_dir / "test.mod.json").write_text(
+        json.dumps({"module": "test.mod", "content": {}}),
+        encoding="utf-8",
+    )
+
+    return mcp_root
+
+
+@pytest.fixture
+def mock_mcp_server_run(monkeypatch):
+    """
+    Mock MCPServer.run so no real server is started.
+    """
+    called = {"value": False}
+
+    def fake_run(self, transport="streamable-http"):
+        called["value"] = True
+
+    monkeypatch.setattr(
+        "docforge.servers.MCPServer.run",
+        fake_run,
+    )
+
+    return lambda: called["value"]