site name correct position

- 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

@@ -22,5 +22,7 @@ groups:
     - docforge/cli/index.md
     - docforge/cli/main.md
     - docforge/cli/commands.md
-    - docforge/cli/mcp_utils.md
-    - docforge/cli/mkdocs_utils.md
+    - docforge/cli/mcp/index.md
+    - docforge/cli/mcp/logic.md
+    - docforge/cli/mkdocs/index.md
+    - docforge/cli/mkdocs/logic.md

docforge/__init__.py

@@ -6,12 +6,6 @@ speed, flexibility, and beautiful output. It decouples the introspection of
 your code from the rendering process, allowing you to generate documentation
 for various platforms (starting with MkDocs) from a single internal models.
 
-## Available Commands
-
-- **build**: Build documentation (MkDocs site or MCP resources).
-- **serve**: Serve documentation (MkDocs or MCP).
-- **tree**: Visualize the introspected project structure.
-
 ## Installation
 
 Install using `pip` with the optional `mkdocs` dependencies for a complete setup:
@@ -22,14 +16,10 @@ pip install doc-forge
 
 ## Quick Start
 
-1.  **Build Documentation**:
-    Introspect your package and generate documentation in one step:
+1.  **Generate Markdown Sources**:
+    Introspect your package and create ready-to-use Markdown files:
     ```bash
-    # Build MkDocs site
-    doc-forge build --mkdocs --module my_package --site-name "My Docs"
-
-    # Build MCP resources
-    doc-forge build --mcp --module my_package
+    doc-forge generate --module my_package --docs-dir docs
     ```
 
 2.  **Define Navigation**:
@@ -43,13 +33,14 @@ pip install doc-forge
         - my_package/utils.md
     ```
 
-3.  **Preview**:
+3.  **Generate MkDocs Configuration**:
     ```bash
-    # Serve MkDocs site
-    doc-forge serve --mkdocs
+    doc-forge mkdocs --site-name "My Awesome Docs"
+    ```
 
-    # Serve MCP documentation
-    doc-forge serve --mcp
+4.  **Preview**:
+    ```bash
+    doc-forge serve
     ```
 
 ## Project Structure

docforge/cli/__init__.py

@@ -6,9 +6,11 @@ with doc-forge.
 
 ## Available Commands
 
-- **build**: Build documentation (MkDocs site or MCP resources).
-- **serve**: Serve documentation (MkDocs or MCP).
 - **tree**: Visualize the introspected project structure.
+- **generate**: Create Markdown source files from Python code.
+- **mkdocs**: Generate the primary `mkdocs.yml` configuration.
+- **build**: Build the final documentation site.
+- **serve**: Launch a local development server with live-reloading.
 """
 
 from .main import main

docforge/cli/commands.py

@@ -2,9 +2,8 @@ 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
-
+from docforge.cli.mkdocs import logic as mkdocs_logic
+from docforge.cli.mcp import logic as mcp_logic
 
 @click.group()
 def cli() -> None:
@@ -14,7 +13,6 @@ def cli() -> None:
     """
     pass
 
-
 @cli.command()
 @click.option("--mcp", is_flag=True, help="Build MCP resources")
 @click.option("--mkdocs", is_flag=True, help="Build MkDocs site")
@@ -23,8 +21,7 @@ def cli() -> None:
 # 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("--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
@@ -43,23 +40,6 @@ def build(
 ) -> None:
     """
     Build documentation (MkDocs site or MCP resources).
-
-    This command orchestrates the full build process:
-    1. Introspects the code (Griffe)
-    2. Renders sources (MkDocs Markdown or MCP JSON)
-    3. (MkDocs only) Generates config and runs the final site build.
-
-    Args:
-        mcp: Use the MCP documentation builder.
-        mkdocs: Use the MkDocs documentation builder.
-        module: The dotted path of the module to document.
-        project_name: Optional override for the project name.
-        site_name: (MkDocs) The site display name. Defaults to module name.
-        docs_dir: (MkDocs) Target directory for Markdown sources.
-        nav_file: (MkDocs) Path to the docforge.nav.yml specification.
-        template: (MkDocs) Optional custom mkdocs.yml template.
-        mkdocs_yml: (MkDocs) Target path for the generated mkdocs.yml.
-        out_dir: (MCP) Target directory for MCP JSON resources.
     """
     if not mcp and not mkdocs:
         raise click.UsageError("Must specify either --mcp or --mkdocs")
@@ -71,13 +51,13 @@ def build(
             site_name = module
         
         click.echo(f"Generating MkDocs sources in {docs_dir}...")
-        mkdocs_utils.generate_sources(module, project_name, docs_dir)
+        mkdocs_logic.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)
+        mkdocs_logic.generate_config(docs_dir, nav_file, template, mkdocs_yml, site_name)
         
         click.echo("Running MkDocs build...")
-        mkdocs_utils.build(mkdocs_yml)
+        mkdocs_logic.build(mkdocs_yml)
         click.echo("MkDocs build completed.")
 
     if mcp:
@@ -85,10 +65,9 @@ def build(
             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)
+        mcp_logic.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")
@@ -101,13 +80,7 @@ def serve(
     out_dir: Path,
 ) -> None:
     """
-    Serve documentation (MkDocs or MCP).
-
-    Args:
-        mcp: Serve MCP resources via an MCP server.
-        mkdocs: Serve the MkDocs site using the built-in development server.
-        mkdocs_yml: (MkDocs) Path to the mkdocs.yml configuration.
-        out_dir: (MCP) Path to the mcp_docs/ directory.
+    Serve documentation.
     """
     if mcp and mkdocs:
         raise click.UsageError("Cannot specify both --mcp and --mkdocs")
@@ -115,10 +88,9 @@ def serve(
         raise click.UsageError("Must specify either --mcp or --mkdocs")
 
     if mkdocs:
-        mkdocs_utils.serve(mkdocs_yml)
+        mkdocs_logic.serve(mkdocs_yml)
     elif mcp:
-        mcp_utils.serve(out_dir)
-
+        mcp_logic.serve(out_dir)
 
 @cli.command()
 @click.option(
@@ -136,11 +108,7 @@ def tree(
     project_name: Optional[str],
 ) -> None:
     """
-    Visualize the project structure in the terminal.
-
-    Args:
-        modules: List of module import paths to recursively introspect.
-        project_name: Optional override for the project name shown at the root.
+    Visualize the project structure.
     """
     loader = GriffeLoader()
     project = loader.load_project(list(modules), project_name)
@@ -152,14 +120,9 @@ def tree(
         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 instance to print.
-        indent: Current line indentation (e.g., '│   ').
     """
     click.echo(f"{indent}├── {obj.name}")
     for member in obj.get_all_members():

docforge/cli/commands.pyi

@@ -1,32 +0,0 @@
-from click.core import Group
-from pathlib import Path
-from typing import Sequence, Optional, Any
-
-cli: Group
-
-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: ...
-
-def serve(
-    mcp: bool,
-    mkdocs: bool,
-    mkdocs_yml: Path,
-    out_dir: Path,
-) -> None: ...
-
-def tree(
-    modules: Sequence[str],
-    project_name: Optional[str],
-) -> None: ...
-
-def _print_object(obj: Any, indent: str) -> None: ...

docforge/cli/main.py

@@ -1,6 +1,5 @@
 """
-Main entry point for the doc-forge CLI. This module delegates all command
-execution to docforge.cli.commands.
+Main entry point for the doc-forge CLI.
 """
 from docforge.cli.commands import cli
 

docforge/cli/main.pyi

@@ -1 +0,0 @@
-def main() -> None: ...

docforge/cli/mcp/logic.py

@@ -7,11 +7,6 @@ from docforge.servers import MCPServer
 def generate_resources(module: str, project_name: str | None, out_dir: Path) -> None:
     """
     Generate MCP-compatible documentation resources.
-
-    Args:
-        module: The dotted path of the primary module to document.
-        project_name: Optional override for the project name.
-        out_dir: Directory where the MCP JSON resources and nav will be written.
     """
     loader = GriffeLoader()
     discovered_paths = discover_module_paths(module)
@@ -22,10 +17,7 @@ def generate_resources(module: str, project_name: str | None, out_dir: Path) ->
 
 def serve(mcp_root: Path) -> None:
     """
-    Serve MCP documentation from a pre-built bundle.
-
-    Args:
-        mcp_root: Path to the directory containing index.json, nav.json, and modules/.
+    Serve MCP documentation.
     """
     if not mcp_root.exists():
         raise click.ClickException(f"mcp_docs directory not found: {mcp_root}")

docforge/cli/mcp_utils.pyi

@@ -1,4 +0,0 @@
-from pathlib import Path
-
-def generate_resources(module: str, project_name: str | None, out_dir: Path) -> None: ...
-def serve(mcp_root: Path) -> None: ...

docforge/cli/mkdocs/logic.py

@@ -9,11 +9,6 @@ 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.
-
-    Args:
-        module: The dotted path of the primary module to document.
-        project_name: Optional override for the project name.
-        docs_dir: Directory where the generated Markdown files will be written.
     """
     loader = GriffeLoader()
     discovered_paths = discover_module_paths(module)
@@ -25,13 +20,6 @@ def generate_sources(module: str, project_name: str | None, docs_dir: Path) -> N
 def generate_config(docs_dir: Path, nav_file: Path, template: Path | None, out: Path, site_name: str) -> None:
     """
     Generate an mkdocs.yml configuration 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 (overrides built-in).
-        out: Path where the final mkdocs.yml will be written.
-        site_name: The display name for the documentation site.
     """
     if not nav_file.exists():
         raise click.FileError(str(nav_file), hint="Nav spec not found")
@@ -61,9 +49,6 @@ def generate_config(docs_dir: Path, nav_file: Path, template: Path | None, out:
 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}")
@@ -76,9 +61,6 @@ def build(mkdocs_yml: Path) -> None:
 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}")

docforge/cli/mkdocs_utils.pyi

@@ -1,6 +0,0 @@
-from pathlib import Path
-
-def generate_sources(module: str, project_name: str | None, docs_dir: Path) -> None: ...
-def generate_config(docs_dir: Path, nav_file: Path, template: Path | None, out: Path, site_name: str) -> None: ...
-def build(mkdocs_yml: Path) -> None: ...
-def serve(mkdocs_yml: Path) -> None: ...

docforge/renderers/mcp_renderer.py

@@ -15,10 +15,6 @@ class MCPRenderer:
     def generate_sources(self, project: Project, out_dir: Path) -> None:
         """
         Generate MCP-compatible JSON resources and navigation for the project.
-
-        Args:
-            project: The project model to render.
-            out_dir: Target directory for the generated JSON files.
         """
         modules_dir = out_dir / "modules"
         modules_dir.mkdir(parents=True, exist_ok=True)
@@ -54,11 +50,7 @@ class MCPRenderer:
 
     def _write_module(self, module: Module, modules_dir: Path) -> None:
         """
-        Serialize a module into an MCP JSON resource on disk.
-
-        Args:
-            module: The module instance to serialize.
-            modules_dir: The directory where the module JSON file should be written.
+        Serialize a module into an MCP JSON resource.
         """
         payload = {
             "module": module.path,
@@ -72,12 +64,6 @@ class MCPRenderer:
     def _render_module(self, module: Module) -> Dict:
         """
         Render a Module into MCP-friendly structured data.
-
-        Args:
-            module: The module instance to render.
-
-        Returns:
-            A dictionary following the MCP documentation resource schema.
         """
         data: Dict = {
             "path": module.path,
@@ -93,12 +79,6 @@ class MCPRenderer:
     def _render_object(self, obj: DocObject) -> Dict:
         """
         Recursively render a DocObject into structured MCP data.
-
-        Args:
-            obj: The documented object (class, func, etc.) to render.
-
-        Returns:
-            A dictionary representing the object and its members.
         """
         data: Dict = {
             "name": obj.name,

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/mcp_utils.md

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

docs/docforge/cli/mkdocs/index.md

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

docs/docforge/cli/mkdocs/logic.md

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

docs/docforge/cli/mkdocs_utils.md

@@ -1,3 +0,0 @@
-# Mkdocs Utils
-
-::: docforge.cli.mkdocs_utils

mcp_docs/index.json

@@ -1,6 +1,6 @@
 {
   "project": "docforge",
   "type": "docforge-model",
-  "modules_count": 22,
+  "modules_count": 24,
   "source": "docforge"
 }

mcp_docs/modules/docforge.cli.commands.json

@@ -55,59 +55,59 @@
           }
         }
       },
-      "mkdocs_utils": {
-        "name": "mkdocs_utils",
+      "mkdocs_logic": {
+        "name": "mkdocs_logic",
         "kind": "module",
-        "path": "docforge.cli.commands.mkdocs_utils",
-        "signature": "<bound method Alias.signature of Alias('mkdocs_utils', 'docforge.cli.mkdocs_utils')>",
+        "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_utils.Path",
-            "signature": "<bound method Alias.signature of Alias('Path', 'docforge.cli.mkdocs_utils.Path')>",
+            "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_utils.resources",
-            "signature": "<bound method Alias.signature of Alias('resources', 'docforge.cli.mkdocs_utils.resources')>",
+            "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_utils.click",
-            "signature": "<bound method Alias.signature of Alias('click', 'docforge.cli.mkdocs_utils.click')>",
+            "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_utils.yaml",
-            "signature": "<bound method Alias.signature of Alias('yaml', 'docforge.cli.mkdocs_utils.yaml')>",
+            "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_utils.GriffeLoader",
-            "signature": "<bound method Alias.signature of Alias('GriffeLoader', 'docforge.cli.mkdocs_utils.GriffeLoader')>",
+            "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_utils.GriffeLoader.load_project",
+                "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_utils.GriffeLoader.load_module",
+                "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."
               }
@@ -116,28 +116,28 @@
           "discover_module_paths": {
             "name": "discover_module_paths",
             "kind": "function",
-            "path": "docforge.cli.commands.mkdocs_utils.discover_module_paths",
-            "signature": "<bound method Alias.signature of Alias('discover_module_paths', 'docforge.cli.mkdocs_utils.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.commands.mkdocs_utils.MkDocsRenderer",
-            "signature": "<bound method Alias.signature of Alias('MkDocsRenderer', 'docforge.cli.mkdocs_utils.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.commands.mkdocs_utils.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.commands.mkdocs_utils.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."
               }
@@ -146,28 +146,28 @@
           "load_nav_spec": {
             "name": "load_nav_spec",
             "kind": "function",
-            "path": "docforge.cli.commands.mkdocs_utils.load_nav_spec",
-            "signature": "<bound method Alias.signature of Alias('load_nav_spec', 'docforge.cli.mkdocs_utils.load_nav_spec')>",
+            "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_utils.resolve_nav",
-            "signature": "<bound method Alias.signature of Alias('resolve_nav', 'docforge.cli.mkdocs_utils.resolve_nav')>",
+            "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_utils.MkDocsNavEmitter",
-            "signature": "<bound method Alias.signature of Alias('MkDocsNavEmitter', 'docforge.cli.mkdocs_utils.MkDocsNavEmitter')>",
+            "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_utils.MkDocsNavEmitter.emit",
+                "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."
               }
@@ -176,72 +176,72 @@
           "generate_sources": {
             "name": "generate_sources",
             "kind": "function",
-            "path": "docforge.cli.commands.mkdocs_utils.generate_sources",
-            "signature": "<bound method Alias.signature of Alias('generate_sources', 'docforge.cli.mkdocs_utils.generate_sources')>",
-            "docstring": "Generate Markdown source files for the specified module.\n\nArgs:\n    module: The dotted path of the primary module to document.\n    project_name: Optional override for the project name.\n    docs_dir: Directory where the generated Markdown files will be written."
+            "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_utils.generate_config",
-            "signature": "<bound method Alias.signature of Alias('generate_config', 'docforge.cli.mkdocs_utils.generate_config')>",
-            "docstring": "Generate an mkdocs.yml configuration 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 (overrides built-in).\n    out: Path where the final mkdocs.yml will be written.\n    site_name: The display name for the documentation site."
+            "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_utils.build",
-            "signature": "<bound method Alias.signature of Alias('build', 'docforge.cli.mkdocs_utils.build')>",
-            "docstring": "Build the documentation site using MkDocs.\n\nArgs:\n    mkdocs_yml: Path to the mkdocs.yml configuration file."
+            "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_utils.serve",
-            "signature": "<bound method Alias.signature of Alias('serve', 'docforge.cli.mkdocs_utils.serve')>",
-            "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.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_utils": {
-        "name": "mcp_utils",
+      "mcp_logic": {
+        "name": "mcp_logic",
         "kind": "module",
-        "path": "docforge.cli.commands.mcp_utils",
-        "signature": "<bound method Alias.signature of Alias('mcp_utils', 'docforge.cli.mcp_utils')>",
+        "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_utils.Path",
-            "signature": "<bound method Alias.signature of Alias('Path', 'docforge.cli.mcp_utils.Path')>",
+            "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_utils.click",
-            "signature": "<bound method Alias.signature of Alias('click', 'docforge.cli.mcp_utils.click')>",
+            "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_utils.GriffeLoader",
-            "signature": "<bound method Alias.signature of Alias('GriffeLoader', 'docforge.cli.mcp_utils.GriffeLoader')>",
+            "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_utils.GriffeLoader.load_project",
+                "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_utils.GriffeLoader.load_module",
+                "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."
               }
@@ -250,58 +250,58 @@
           "discover_module_paths": {
             "name": "discover_module_paths",
             "kind": "function",
-            "path": "docforge.cli.commands.mcp_utils.discover_module_paths",
-            "signature": "<bound method Alias.signature of Alias('discover_module_paths', 'docforge.cli.mcp_utils.discover_module_paths')>",
+            "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_utils.MCPRenderer",
-            "signature": "<bound method Alias.signature of Alias('MCPRenderer', 'docforge.cli.mcp_utils.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.commands.mcp_utils.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.commands.mcp_utils.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.\n\nArgs:\n    project: The project model to render.\n    out_dir: Target directory for the generated JSON files."
+                "docstring": "Generate MCP-compatible JSON resources and navigation for the project."
               }
             }
           },
           "MCPServer": {
             "name": "MCPServer",
             "kind": "class",
-            "path": "docforge.cli.commands.mcp_utils.MCPServer",
-            "signature": "<bound method Alias.signature of Alias('MCPServer', 'docforge.cli.mcp_utils.MCPServer')>",
+            "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_utils.MCPServer.mcp_root",
+                "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_utils.MCPServer.app",
+                "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_utils.MCPServer.run",
+                "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)"
               }
@@ -310,60 +310,46 @@
           "generate_resources": {
             "name": "generate_resources",
             "kind": "function",
-            "path": "docforge.cli.commands.mcp_utils.generate_resources",
-            "signature": "<bound method Alias.signature of Alias('generate_resources', 'docforge.cli.mcp_utils.generate_resources')>",
-            "docstring": "Generate MCP-compatible documentation resources.\n\nArgs:\n    module: The dotted path of the primary module to document.\n    project_name: Optional override for the project name.\n    out_dir: Directory where the MCP JSON resources and nav will be written."
+            "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_utils.serve",
-            "signature": "<bound method Alias.signature of Alias('serve', 'docforge.cli.mcp_utils.serve')>",
-            "docstring": "Serve MCP documentation from a pre-built bundle.\n\nArgs:\n    mcp_root: Path to the directory containing index.json, nav.json, and modules/."
+            "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": "attribute",
+        "kind": "function",
         "path": "docforge.cli.commands.cli",
-        "signature": null,
-        "docstring": null
+        "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', 18, 89)>",
-        "docstring": "Build documentation (MkDocs site or MCP resources).\n\nThis command orchestrates the full build process:\n1. Introspects the code (Griffe)\n2. Renders sources (MkDocs Markdown or MCP JSON)\n3. (MkDocs only) Generates config and runs the final site build.\n\nArgs:\n    mcp: Use the MCP documentation builder.\n    mkdocs: Use the MkDocs documentation builder.\n    module: The dotted path of the module to document.\n    project_name: Optional override for the project name.\n    site_name: (MkDocs) The site display name. Defaults to module name.\n    docs_dir: (MkDocs) Target directory for Markdown sources.\n    nav_file: (MkDocs) Path to the docforge.nav.yml specification.\n    template: (MkDocs) Optional custom mkdocs.yml template.\n    mkdocs_yml: (MkDocs) Target path for the generated mkdocs.yml.\n    out_dir: (MCP) Target directory for MCP JSON resources."
+        "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', 92, 120)>",
-        "docstring": "Serve documentation (MkDocs or MCP).\n\nArgs:\n    mcp: Serve MCP resources via an MCP server.\n    mkdocs: Serve the MkDocs site using the built-in development server.\n    mkdocs_yml: (MkDocs) Path to the mkdocs.yml configuration.\n    out_dir: (MCP) Path to the mcp_docs/ directory."
+        "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', 123, 153)>",
-        "docstring": "Visualize the project structure in the terminal.\n\nArgs:\n    modules: List of module import paths to recursively introspect.\n    project_name: Optional override for the project name shown at the root."
-      },
-      "Group": {
-        "name": "Group",
-        "kind": "alias",
-        "path": "docforge.cli.commands.Group",
-        "signature": "<bound method Alias.signature of Alias('Group', 'click.core.Group')>",
-        "docstring": null
-      },
-      "Any": {
-        "name": "Any",
-        "kind": "alias",
-        "path": "docforge.cli.commands.Any",
-        "signature": "<bound method Alias.signature of Alias('Any', 'typing.Any')>",
-        "docstring": null
+        "signature": "<bound method Function.signature of Function('tree', 95, 121)>",
+        "docstring": "Visualize the project structure."
       }
     }
   }

mcp_docs/modules/docforge.cli.json

@@ -2,27 +2,27 @@
   "module": "docforge.cli",
   "content": {
     "path": "docforge.cli",
-    "docstring": "# CLI Layer\n\nThe `docforge.cli` package provides the command-line interface for interacting\nwith doc-forge.\n\n## Available Commands\n\n- **build**: Build documentation (MkDocs site or MCP resources).\n- **serve**: Serve documentation (MkDocs or MCP).\n- **tree**: Visualize the introspected project structure.",
+    "docstring": "# CLI Layer\n\nThe `docforge.cli` package provides the command-line interface for interacting\nwith doc-forge.\n\n## Available Commands\n\n- **tree**: Visualize the introspected project structure.\n- **generate**: Create Markdown source files from Python code.\n- **mkdocs**: Generate the primary `mkdocs.yml` configuration.\n- **build**: Build the final documentation site.\n- **serve**: Launch a local development server with live-reloading.",
     "objects": {
       "main": {
         "name": "main",
         "kind": "module",
         "path": "docforge.cli.main",
         "signature": null,
-        "docstring": "Main entry point for the doc-forge CLI. This module delegates all command\nexecution to docforge.cli.commands.",
+        "docstring": "Main entry point for the doc-forge CLI.",
         "members": {
           "cli": {
             "name": "cli",
-            "kind": "attribute",
+            "kind": "function",
             "path": "docforge.cli.main.cli",
             "signature": "<bound method Alias.signature of Alias('cli', 'docforge.cli.commands.cli')>",
-            "docstring": null
+            "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', 7, 11)>",
+            "signature": "<bound method Function.signature of Function('main', 6, 10)>",
             "docstring": "CLI Entry point. Boots the click application."
           }
         }
@@ -85,59 +85,59 @@
               }
             }
           },
-          "mkdocs_utils": {
-            "name": "mkdocs_utils",
+          "mkdocs_logic": {
+            "name": "mkdocs_logic",
             "kind": "module",
-            "path": "docforge.cli.commands.mkdocs_utils",
-            "signature": "<bound method Alias.signature of Alias('mkdocs_utils', 'docforge.cli.mkdocs_utils')>",
+            "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_utils.Path",
-                "signature": "<bound method Alias.signature of Alias('Path', 'docforge.cli.mkdocs_utils.Path')>",
+                "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_utils.resources",
-                "signature": "<bound method Alias.signature of Alias('resources', 'docforge.cli.mkdocs_utils.resources')>",
+                "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_utils.click",
-                "signature": "<bound method Alias.signature of Alias('click', 'docforge.cli.mkdocs_utils.click')>",
+                "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_utils.yaml",
-                "signature": "<bound method Alias.signature of Alias('yaml', 'docforge.cli.mkdocs_utils.yaml')>",
+                "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_utils.GriffeLoader",
-                "signature": "<bound method Alias.signature of Alias('GriffeLoader', 'docforge.cli.mkdocs_utils.GriffeLoader')>",
+                "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_utils.GriffeLoader.load_project",
+                    "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_utils.GriffeLoader.load_module",
+                    "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."
                   }
@@ -146,28 +146,28 @@
               "discover_module_paths": {
                 "name": "discover_module_paths",
                 "kind": "function",
-                "path": "docforge.cli.commands.mkdocs_utils.discover_module_paths",
-                "signature": "<bound method Alias.signature of Alias('discover_module_paths', 'docforge.cli.mkdocs_utils.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.commands.mkdocs_utils.MkDocsRenderer",
-                "signature": "<bound method Alias.signature of Alias('MkDocsRenderer', 'docforge.cli.mkdocs_utils.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.commands.mkdocs_utils.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.commands.mkdocs_utils.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."
                   }
@@ -176,28 +176,28 @@
               "load_nav_spec": {
                 "name": "load_nav_spec",
                 "kind": "function",
-                "path": "docforge.cli.commands.mkdocs_utils.load_nav_spec",
-                "signature": "<bound method Alias.signature of Alias('load_nav_spec', 'docforge.cli.mkdocs_utils.load_nav_spec')>",
+                "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_utils.resolve_nav",
-                "signature": "<bound method Alias.signature of Alias('resolve_nav', 'docforge.cli.mkdocs_utils.resolve_nav')>",
+                "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_utils.MkDocsNavEmitter",
-                "signature": "<bound method Alias.signature of Alias('MkDocsNavEmitter', 'docforge.cli.mkdocs_utils.MkDocsNavEmitter')>",
+                "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_utils.MkDocsNavEmitter.emit",
+                    "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."
                   }
@@ -206,72 +206,72 @@
               "generate_sources": {
                 "name": "generate_sources",
                 "kind": "function",
-                "path": "docforge.cli.commands.mkdocs_utils.generate_sources",
-                "signature": "<bound method Alias.signature of Alias('generate_sources', 'docforge.cli.mkdocs_utils.generate_sources')>",
-                "docstring": "Generate Markdown source files for the specified module.\n\nArgs:\n    module: The dotted path of the primary module to document.\n    project_name: Optional override for the project name.\n    docs_dir: Directory where the generated Markdown files will be written."
+                "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_utils.generate_config",
-                "signature": "<bound method Alias.signature of Alias('generate_config', 'docforge.cli.mkdocs_utils.generate_config')>",
-                "docstring": "Generate an mkdocs.yml configuration 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 (overrides built-in).\n    out: Path where the final mkdocs.yml will be written.\n    site_name: The display name for the documentation site."
+                "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_utils.build",
-                "signature": "<bound method Alias.signature of Alias('build', 'docforge.cli.mkdocs_utils.build')>",
-                "docstring": "Build the documentation site using MkDocs.\n\nArgs:\n    mkdocs_yml: Path to the mkdocs.yml configuration file."
+                "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_utils.serve",
-                "signature": "<bound method Alias.signature of Alias('serve', 'docforge.cli.mkdocs_utils.serve')>",
-                "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.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_utils": {
-            "name": "mcp_utils",
+          "mcp_logic": {
+            "name": "mcp_logic",
             "kind": "module",
-            "path": "docforge.cli.commands.mcp_utils",
-            "signature": "<bound method Alias.signature of Alias('mcp_utils', 'docforge.cli.mcp_utils')>",
+            "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_utils.Path",
-                "signature": "<bound method Alias.signature of Alias('Path', 'docforge.cli.mcp_utils.Path')>",
+                "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_utils.click",
-                "signature": "<bound method Alias.signature of Alias('click', 'docforge.cli.mcp_utils.click')>",
+                "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_utils.GriffeLoader",
-                "signature": "<bound method Alias.signature of Alias('GriffeLoader', 'docforge.cli.mcp_utils.GriffeLoader')>",
+                "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_utils.GriffeLoader.load_project",
+                    "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_utils.GriffeLoader.load_module",
+                    "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."
                   }
@@ -280,58 +280,58 @@
               "discover_module_paths": {
                 "name": "discover_module_paths",
                 "kind": "function",
-                "path": "docforge.cli.commands.mcp_utils.discover_module_paths",
-                "signature": "<bound method Alias.signature of Alias('discover_module_paths', 'docforge.cli.mcp_utils.discover_module_paths')>",
+                "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_utils.MCPRenderer",
-                "signature": "<bound method Alias.signature of Alias('MCPRenderer', 'docforge.cli.mcp_utils.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.commands.mcp_utils.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.commands.mcp_utils.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.\n\nArgs:\n    project: The project model to render.\n    out_dir: Target directory for the generated JSON files."
+                    "docstring": "Generate MCP-compatible JSON resources and navigation for the project."
                   }
                 }
               },
               "MCPServer": {
                 "name": "MCPServer",
                 "kind": "class",
-                "path": "docforge.cli.commands.mcp_utils.MCPServer",
-                "signature": "<bound method Alias.signature of Alias('MCPServer', 'docforge.cli.mcp_utils.MCPServer')>",
+                "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_utils.MCPServer.mcp_root",
+                    "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_utils.MCPServer.app",
+                    "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_utils.MCPServer.run",
+                    "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)"
                   }
@@ -340,328 +340,332 @@
               "generate_resources": {
                 "name": "generate_resources",
                 "kind": "function",
-                "path": "docforge.cli.commands.mcp_utils.generate_resources",
-                "signature": "<bound method Alias.signature of Alias('generate_resources', 'docforge.cli.mcp_utils.generate_resources')>",
-                "docstring": "Generate MCP-compatible documentation resources.\n\nArgs:\n    module: The dotted path of the primary module to document.\n    project_name: Optional override for the project name.\n    out_dir: Directory where the MCP JSON resources and nav will be written."
+                "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_utils.serve",
-                "signature": "<bound method Alias.signature of Alias('serve', 'docforge.cli.mcp_utils.serve')>",
-                "docstring": "Serve MCP documentation from a pre-built bundle.\n\nArgs:\n    mcp_root: Path to the directory containing index.json, nav.json, and modules/."
+                "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": "attribute",
+            "kind": "function",
             "path": "docforge.cli.commands.cli",
-            "signature": null,
-            "docstring": null
+            "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', 18, 89)>",
-            "docstring": "Build documentation (MkDocs site or MCP resources).\n\nThis command orchestrates the full build process:\n1. Introspects the code (Griffe)\n2. Renders sources (MkDocs Markdown or MCP JSON)\n3. (MkDocs only) Generates config and runs the final site build.\n\nArgs:\n    mcp: Use the MCP documentation builder.\n    mkdocs: Use the MkDocs documentation builder.\n    module: The dotted path of the module to document.\n    project_name: Optional override for the project name.\n    site_name: (MkDocs) The site display name. Defaults to module name.\n    docs_dir: (MkDocs) Target directory for Markdown sources.\n    nav_file: (MkDocs) Path to the docforge.nav.yml specification.\n    template: (MkDocs) Optional custom mkdocs.yml template.\n    mkdocs_yml: (MkDocs) Target path for the generated mkdocs.yml.\n    out_dir: (MCP) Target directory for MCP JSON resources."
+            "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', 92, 120)>",
-            "docstring": "Serve documentation (MkDocs or MCP).\n\nArgs:\n    mcp: Serve MCP resources via an MCP server.\n    mkdocs: Serve the MkDocs site using the built-in development server.\n    mkdocs_yml: (MkDocs) Path to the mkdocs.yml configuration.\n    out_dir: (MCP) Path to the mcp_docs/ directory."
+            "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', 123, 153)>",
-            "docstring": "Visualize the project structure in the terminal.\n\nArgs:\n    modules: List of module import paths to recursively introspect.\n    project_name: Optional override for the project name shown at the root."
-          },
-          "Group": {
-            "name": "Group",
-            "kind": "alias",
-            "path": "docforge.cli.commands.Group",
-            "signature": "<bound method Alias.signature of Alias('Group', 'click.core.Group')>",
-            "docstring": null
-          },
-          "Any": {
-            "name": "Any",
-            "kind": "alias",
-            "path": "docforge.cli.commands.Any",
-            "signature": "<bound method Alias.signature of Alias('Any', 'typing.Any')>",
-            "docstring": null
+            "signature": "<bound method Function.signature of Function('tree', 95, 121)>",
+            "docstring": "Visualize the project structure."
           }
         }
       },
-      "mcp_utils": {
-        "name": "mcp_utils",
+      "mcp": {
+        "name": "mcp",
         "kind": "module",
-        "path": "docforge.cli.mcp_utils",
+        "path": "docforge.cli.mcp",
         "signature": null,
         "docstring": null,
         "members": {
-          "Path": {
-            "name": "Path",
-            "kind": "alias",
-            "path": "docforge.cli.mcp_utils.Path",
-            "signature": "<bound method Alias.signature of Alias('Path', 'pathlib.Path')>",
-            "docstring": null
-          },
-          "click": {
-            "name": "click",
-            "kind": "alias",
-            "path": "docforge.cli.mcp_utils.click",
-            "signature": "<bound method Alias.signature of Alias('click', 'click')>",
-            "docstring": null
-          },
-          "GriffeLoader": {
-            "name": "GriffeLoader",
-            "kind": "class",
-            "path": "docforge.cli.mcp_utils.GriffeLoader",
-            "signature": "<bound method Alias.signature of Alias('GriffeLoader', 'docforge.loaders.GriffeLoader')>",
-            "docstring": "Loads Python modules and extracts documentation using the Griffe introspection engine.",
+          "logic": {
+            "name": "logic",
+            "kind": "module",
+            "path": "docforge.cli.mcp.logic",
+            "signature": null,
+            "docstring": null,
             "members": {
-              "load_project": {
-                "name": "load_project",
-                "kind": "function",
-                "path": "docforge.cli.mcp_utils.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."
+              "Path": {
+                "name": "Path",
+                "kind": "alias",
+                "path": "docforge.cli.mcp.logic.Path",
+                "signature": "<bound method Alias.signature of Alias('Path', 'pathlib.Path')>",
+                "docstring": null
               },
-              "load_module": {
-                "name": "load_module",
+              "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_utils.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."
+                "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."
               }
             }
-          },
-          "discover_module_paths": {
-            "name": "discover_module_paths",
-            "kind": "function",
-            "path": "docforge.cli.mcp_utils.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_utils.MCPRenderer",
-            "signature": "<bound method Alias.signature of Alias('MCPRenderer', 'docforge.renderers.MCPRenderer')>",
-            "docstring": "Renderer that emits MCP-native JSON resources from docforge models.",
+          }
+        }
+      },
+      "mkdocs": {
+        "name": "mkdocs",
+        "kind": "module",
+        "path": "docforge.cli.mkdocs",
+        "signature": null,
+        "docstring": null,
+        "members": {
+          "logic": {
+            "name": "logic",
+            "kind": "module",
+            "path": "docforge.cli.mkdocs.logic",
+            "signature": null,
+            "docstring": null,
             "members": {
-              "name": {
-                "name": "name",
-                "kind": "attribute",
-                "path": "docforge.cli.mcp_utils.MCPRenderer.name",
-                "signature": "<bound method Alias.signature of Alias('name', 'docforge.renderers.mcp_renderer.MCPRenderer.name')>",
+              "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.mcp_utils.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.\n\nArgs:\n    project: The project model to render.\n    out_dir: Target directory for the generated JSON files."
-              }
-            }
-          },
-          "MCPServer": {
-            "name": "MCPServer",
-            "kind": "class",
-            "path": "docforge.cli.mcp_utils.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_utils.MCPServer.mcp_root",
-                "signature": "<bound method Alias.signature of Alias('mcp_root', 'docforge.servers.mcp_server.MCPServer.mcp_root')>",
-                "docstring": null
+                "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."
               },
-              "app": {
-                "name": "app",
-                "kind": "attribute",
-                "path": "docforge.cli.mcp_utils.MCPServer.app",
-                "signature": "<bound method Alias.signature of Alias('app', 'docforge.servers.mcp_server.MCPServer.app')>",
-                "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."
               },
-              "run": {
-                "name": "run",
+              "build": {
+                "name": "build",
                 "kind": "function",
-                "path": "docforge.cli.mcp_utils.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_utils.generate_resources",
-            "signature": "<bound method Function.signature of Function('generate_resources', 7, 21)>",
-            "docstring": "Generate MCP-compatible documentation resources.\n\nArgs:\n    module: The dotted path of the primary module to document.\n    project_name: Optional override for the project name.\n    out_dir: Directory where the MCP JSON resources and nav will be written."
-          },
-          "serve": {
-            "name": "serve",
-            "kind": "function",
-            "path": "docforge.cli.mcp_utils.serve",
-            "signature": "<bound method Function.signature of Function('serve', 23, 47)>",
-            "docstring": "Serve MCP documentation from a pre-built bundle.\n\nArgs:\n    mcp_root: Path to the directory containing index.json, nav.json, and modules/."
-          }
-        }
-      },
-      "mkdocs_utils": {
-        "name": "mkdocs_utils",
-        "kind": "module",
-        "path": "docforge.cli.mkdocs_utils",
-        "signature": null,
-        "docstring": null,
-        "members": {
-          "Path": {
-            "name": "Path",
-            "kind": "alias",
-            "path": "docforge.cli.mkdocs_utils.Path",
-            "signature": "<bound method Alias.signature of Alias('Path', 'pathlib.Path')>",
-            "docstring": null
-          },
-          "resources": {
-            "name": "resources",
-            "kind": "alias",
-            "path": "docforge.cli.mkdocs_utils.resources",
-            "signature": "<bound method Alias.signature of Alias('resources', 'importlib.resources')>",
-            "docstring": null
-          },
-          "click": {
-            "name": "click",
-            "kind": "alias",
-            "path": "docforge.cli.mkdocs_utils.click",
-            "signature": "<bound method Alias.signature of Alias('click', 'click')>",
-            "docstring": null
-          },
-          "yaml": {
-            "name": "yaml",
-            "kind": "alias",
-            "path": "docforge.cli.mkdocs_utils.yaml",
-            "signature": "<bound method Alias.signature of Alias('yaml', 'yaml')>",
-            "docstring": null
-          },
-          "GriffeLoader": {
-            "name": "GriffeLoader",
-            "kind": "class",
-            "path": "docforge.cli.mkdocs_utils.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_utils.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."
+                "path": "docforge.cli.mkdocs.logic.build",
+                "signature": "<bound method Function.signature of Function('build', 49, 59)>",
+                "docstring": "Build the documentation site using MkDocs."
               },
-              "load_module": {
-                "name": "load_module",
+              "serve": {
+                "name": "serve",
                 "kind": "function",
-                "path": "docforge.cli.mkdocs_utils.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."
+                "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."
               }
             }
-          },
-          "discover_module_paths": {
-            "name": "discover_module_paths",
-            "kind": "function",
-            "path": "docforge.cli.mkdocs_utils.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_utils.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_utils.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_utils.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_utils.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_utils.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_utils.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_utils.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_utils.generate_sources",
-            "signature": "<bound method Function.signature of Function('generate_sources', 9, 23)>",
-            "docstring": "Generate Markdown source files for the specified module.\n\nArgs:\n    module: The dotted path of the primary module to document.\n    project_name: Optional override for the project name.\n    docs_dir: Directory where the generated Markdown files will be written."
-          },
-          "generate_config": {
-            "name": "generate_config",
-            "kind": "function",
-            "path": "docforge.cli.mkdocs_utils.generate_config",
-            "signature": "<bound method Function.signature of Function('generate_config', 25, 59)>",
-            "docstring": "Generate an mkdocs.yml configuration 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 (overrides built-in).\n    out: Path where the final mkdocs.yml will be written.\n    site_name: The display name for the documentation site."
-          },
-          "build": {
-            "name": "build",
-            "kind": "function",
-            "path": "docforge.cli.mkdocs_utils.build",
-            "signature": "<bound method Function.signature of Function('build', 61, 74)>",
-            "docstring": "Build the documentation site using MkDocs.\n\nArgs:\n    mkdocs_yml: Path to the mkdocs.yml configuration file."
-          },
-          "serve": {
-            "name": "serve",
-            "kind": "function",
-            "path": "docforge.cli.mkdocs_utils.serve",
-            "signature": "<bound method Function.signature of Function('serve', 76, 87)>",
-            "docstring": "Serve the documentation site with live-reload using MkDocs.\n\nArgs:\n    mkdocs_yml: Path to the mkdocs.yml configuration file."
           }
         }
       }

mcp_docs/modules/docforge.cli.main.json

@@ -2,20 +2,20 @@
   "module": "docforge.cli.main",
   "content": {
     "path": "docforge.cli.main",
-    "docstring": "Main entry point for the doc-forge CLI. This module delegates all command\nexecution to docforge.cli.commands.",
+    "docstring": "Main entry point for the doc-forge CLI.",
     "objects": {
       "cli": {
         "name": "cli",
-        "kind": "attribute",
+        "kind": "function",
         "path": "docforge.cli.main.cli",
         "signature": "<bound method Alias.signature of Alias('cli', 'docforge.cli.commands.cli')>",
-        "docstring": null
+        "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', 7, 11)>",
+        "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

@@ -1,41 +1,41 @@
 {
-  "module": "docforge.cli.mcp_utils",
+  "module": "docforge.cli.mcp.logic",
   "content": {
-    "path": "docforge.cli.mcp_utils",
+    "path": "docforge.cli.mcp.logic",
     "docstring": null,
     "objects": {
       "Path": {
         "name": "Path",
         "kind": "alias",
-        "path": "docforge.cli.mcp_utils.Path",
+        "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_utils.click",
+        "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_utils.GriffeLoader",
+        "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_utils.GriffeLoader.load_project",
+            "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_utils.GriffeLoader.load_module",
+            "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."
           }
@@ -44,58 +44,58 @@
       "discover_module_paths": {
         "name": "discover_module_paths",
         "kind": "function",
-        "path": "docforge.cli.mcp_utils.discover_module_paths",
+        "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_utils.MCPRenderer",
+        "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_utils.MCPRenderer.name",
+            "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_utils.MCPRenderer.generate_sources",
+            "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.\n\nArgs:\n    project: The project model to render.\n    out_dir: Target directory for the generated JSON files."
+            "docstring": "Generate MCP-compatible JSON resources and navigation for the project."
           }
         }
       },
       "MCPServer": {
         "name": "MCPServer",
         "kind": "class",
-        "path": "docforge.cli.mcp_utils.MCPServer",
+        "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_utils.MCPServer.mcp_root",
+            "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_utils.MCPServer.app",
+            "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_utils.MCPServer.run",
+            "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)"
           }
@@ -104,16 +104,16 @@
       "generate_resources": {
         "name": "generate_resources",
         "kind": "function",
-        "path": "docforge.cli.mcp_utils.generate_resources",
-        "signature": "<bound method Function.signature of Function('generate_resources', 7, 21)>",
-        "docstring": "Generate MCP-compatible documentation resources.\n\nArgs:\n    module: The dotted path of the primary module to document.\n    project_name: Optional override for the project name.\n    out_dir: Directory where the MCP JSON resources and nav will be written."
+        "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_utils.serve",
-        "signature": "<bound method Function.signature of Function('serve', 23, 47)>",
-        "docstring": "Serve MCP documentation from a pre-built bundle.\n\nArgs:\n    mcp_root: Path to the directory containing index.json, nav.json, and modules/."
+        "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

@@ -0,0 +1,157 @@
+{
+  "module": "docforge.cli.mkdocs",
+  "content": {
+    "path": "docforge.cli.mkdocs",
+    "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.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.cli.mkdocs.logic.json

@@ -1,55 +1,55 @@
 {
-  "module": "docforge.cli.mkdocs_utils",
+  "module": "docforge.cli.mkdocs.logic",
   "content": {
-    "path": "docforge.cli.mkdocs_utils",
+    "path": "docforge.cli.mkdocs.logic",
     "docstring": null,
     "objects": {
       "Path": {
         "name": "Path",
         "kind": "alias",
-        "path": "docforge.cli.mkdocs_utils.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_utils.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_utils.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_utils.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_utils.GriffeLoader",
+        "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_utils.GriffeLoader.load_project",
+            "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_utils.GriffeLoader.load_module",
+            "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."
           }
@@ -58,28 +58,28 @@
       "discover_module_paths": {
         "name": "discover_module_paths",
         "kind": "function",
-        "path": "docforge.cli.mkdocs_utils.discover_module_paths",
+        "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_utils.MkDocsRenderer",
+        "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_utils.MkDocsRenderer.name",
+            "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_utils.MkDocsRenderer.generate_sources",
+            "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."
           }
@@ -88,28 +88,28 @@
       "load_nav_spec": {
         "name": "load_nav_spec",
         "kind": "function",
-        "path": "docforge.cli.mkdocs_utils.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_utils.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_utils.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_utils.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."
           }
@@ -118,30 +118,30 @@
       "generate_sources": {
         "name": "generate_sources",
         "kind": "function",
-        "path": "docforge.cli.mkdocs_utils.generate_sources",
-        "signature": "<bound method Function.signature of Function('generate_sources', 9, 23)>",
-        "docstring": "Generate Markdown source files for the specified module.\n\nArgs:\n    module: The dotted path of the primary module to document.\n    project_name: Optional override for the project name.\n    docs_dir: Directory where the generated Markdown files will be written."
+        "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_utils.generate_config",
-        "signature": "<bound method Function.signature of Function('generate_config', 25, 59)>",
-        "docstring": "Generate an mkdocs.yml configuration 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 (overrides built-in).\n    out: Path where the final mkdocs.yml will be written.\n    site_name: The display name for the documentation site."
+        "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_utils.build",
-        "signature": "<bound method Function.signature of Function('build', 61, 74)>",
-        "docstring": "Build the documentation site using MkDocs.\n\nArgs:\n    mkdocs_yml: Path to the mkdocs.yml configuration file."
+        "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_utils.serve",
-        "signature": "<bound method Function.signature of Function('serve', 76, 87)>",
-        "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.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.renderers.json

@@ -46,7 +46,7 @@
             "kind": "function",
             "path": "docforge.renderers.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.\n\nArgs:\n    project: The project model to render.\n    out_dir: Target directory for the generated JSON files."
+            "docstring": "Generate MCP-compatible JSON resources and navigation for the project."
           }
         }
       },
@@ -383,7 +383,7 @@
             "name": "MCPRenderer",
             "kind": "class",
             "path": "docforge.renderers.mcp_renderer.MCPRenderer",
-            "signature": "<bound method Class.signature of Class('MCPRenderer', 8, 122)>",
+            "signature": "<bound method Class.signature of Class('MCPRenderer', 8, 102)>",
             "docstring": "Renderer that emits MCP-native JSON resources from docforge models.",
             "members": {
               "name": {
@@ -397,8 +397,8 @@
                 "name": "generate_sources",
                 "kind": "function",
                 "path": "docforge.renderers.mcp_renderer.MCPRenderer.generate_sources",
-                "signature": "<bound method Function.signature of Function('generate_sources', 15, 53)>",
-                "docstring": "Generate MCP-compatible JSON resources and navigation for the project.\n\nArgs:\n    project: The project model to render.\n    out_dir: Target directory for the generated JSON files."
+                "signature": "<bound method Function.signature of Function('generate_sources', 15, 49)>",
+                "docstring": "Generate MCP-compatible JSON resources and navigation for the project."
               }
             }
           }

mcp_docs/modules/docforge.renderers.mcp_renderer.json

@@ -210,7 +210,7 @@
         "name": "MCPRenderer",
         "kind": "class",
         "path": "docforge.renderers.mcp_renderer.MCPRenderer",
-        "signature": "<bound method Class.signature of Class('MCPRenderer', 8, 122)>",
+        "signature": "<bound method Class.signature of Class('MCPRenderer', 8, 102)>",
         "docstring": "Renderer that emits MCP-native JSON resources from docforge models.",
         "members": {
           "name": {
@@ -224,8 +224,8 @@
             "name": "generate_sources",
             "kind": "function",
             "path": "docforge.renderers.mcp_renderer.MCPRenderer.generate_sources",
-            "signature": "<bound method Function.signature of Function('generate_sources', 15, 53)>",
-            "docstring": "Generate MCP-compatible JSON resources and navigation for the project.\n\nArgs:\n    project: The project model to render.\n    out_dir: Target directory for the generated JSON files."
+            "signature": "<bound method Function.signature of Function('generate_sources', 15, 49)>",
+            "docstring": "Generate MCP-compatible JSON resources and navigation for the project."
           }
         }
       }

mcp_docs/nav.json

@@ -16,12 +16,20 @@
     "resource": "doc://modules/docforge.cli.main"
   },
   {
-    "module": "docforge.cli.mcp_utils",
-    "resource": "doc://modules/docforge.cli.mcp_utils"
+    "module": "docforge.cli.mcp",
+    "resource": "doc://modules/docforge.cli.mcp"
   },
   {
-    "module": "docforge.cli.mkdocs_utils",
-    "resource": "doc://modules/docforge.cli.mkdocs_utils"
+    "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",

mkdocs.yml

@@ -58,5 +58,7 @@ nav:
   - docforge/cli/index.md
   - docforge/cli/main.md
   - docforge/cli/commands.md
-  - docforge/cli/mcp_utils.md
-  - docforge/cli/mkdocs_utils.md
+  - docforge/cli/mcp/index.md
+  - docforge/cli/mcp/logic.md
+  - docforge/cli/mkdocs/index.md
+  - docforge/cli/mkdocs/logic.md

pyproject.toml

@@ -5,7 +5,7 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "doc-forge"
-version = "0.0.3"
+version = "0.0.2"
 description = "A renderer-agnostic Python documentation compiler"
 readme = "README.md"
 requires-python = ">=3.10"

tests/cli/test_build_mcp.py

@@ -1,4 +1,6 @@
+import json
 from pathlib import Path
+from click.testing import CliRunner
 from docforge.cli.main import cli
 
 def test_mcp_build(cli_runner):

tests/cli/test_build_mkdocs.py

@@ -48,52 +48,7 @@ def test_mkdocs_build_missing_module_fails(cli_runner):
     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()
+def test_mkdocs_build_missing_site_name_fails(cli_runner):
+    result = cli_runner.invoke(cli, ["build", "--mkdocs", "--module", "testpkg"])
+    assert result.exit_code != 0
+    assert "--site-name is required" in result.output