doc string changes with sample to generate doc strings for packages/modules

# Merge Request: Flatten MkDocs Structure + `--module-is-source` Support

## Summary

This MR introduces structural improvements to the MkDocs generation pipeline to:

1. Ensure a root `docs/index.md` always exists
2. Flatten documentation structure (remove `docs/<module>/` nesting by default)
3. Add support for `--module-is-source` to treat the module as the documentation root
4. Align navigation (`docforge.nav.yml`) with the new flat layout
5. Regenerate MCP artifacts to reflect updated signatures and docstrings

This resolves static hosting issues (e.g., Nginx 403 due to missing `site/index.html`) and makes each generated MkDocs site deployable as a standalone static website.

---

## Motivation

Previously, documentation was generated under:

```
docs/<module>/...
```

Which resulted in:

```
site/<module>/index.html
```

When deployed at `/libs/<project>/`, this caused:

* Missing `site/index.html`
* Nginx returning 403 for root access
* Inconsistent static hosting behavior

This MR corrects the architecture so each MkDocs build is a valid static site with a root entry point.

---

## Key Changes

### 1️⃣ Flattened Docs Structure

**Before**

```
docs/docforge/index.md
```

**After**

```
docs/index.md
```

All documentation paths were updated accordingly:

* `docs/docforge/cli/...` → `docs/cli/...`
* `docs/docforge/models/...` → `docs/models/...`
* `docs/docforge/renderers/...` → `docs/renderers/...`

Navigation updated to match the flat layout.

---

### 2️⃣ Root Index Enforcement

`MkDocsRenderer` now guarantees:

* `docs/index.md` is always created
* Parent `index.md` files are auto-generated if missing
* Parent indexes link to child modules (idempotent behavior)

This ensures:

```
site/index.html
```

Always exists after `mkdocs build`.

---

### 3️⃣ New CLI Flag: `--module-is-source`

Added option:

```
--module-is-source
```

Behavior:

* Treats the provided module as the documentation root
* Removes the top-level module folder from generated paths
* Prevents redundant nesting when the module corresponds to the source root

Updated components:

* `cli.commands.build`
* `mkdocs_utils.generate_sources`
* `MkDocsRenderer.generate_sources`
* Stub files (`.pyi`)
* MCP JSON artifacts

---

### 4️⃣ Navigation Spec Update

`docforge.nav.yml` updated:

**Before**

```yaml
home: docforge/index.md
```

**After**

```yaml
home: index.md
```

All group paths adjusted to remove `docforge/` prefix.

---

### 5️⃣ MkDocs Config Update

`mkdocs.yml` updated to:

* Move `site_name` below theme/plugins
* Use flat navigation paths
* Point Home to `index.md`

---

### 6️⃣ MCP Artifact Regeneration

Updated:

* Function signatures (new parameter)
* Docstrings (reflect `module_is_source`)
* Renderer metadata
* Line numbers

Ensures MCP output matches updated API.

---

## Architectural Outcome

Each project now produces a **valid standalone static site**:

```
site/
  index.html
  assets/
  search/
```

Safe for deployment under:

```
/libs/<project>/
```

No Nginx rewrites required.
No directory-index issues.
No nested-site ambiguity.

---

## Backward Compatibility

* Existing CLI usage remains valid
* `--module-is-source` is optional
* Navigation spec format unchanged (only paths adjusted)

---

## Deployment Impact

After merge:

* Each library can be deployed independently
* Sites can be merged under a shared root without internal conflicts
* Static hosting is predictable and production-safe

---

## Testing

* Verified MkDocs build produces `site/index.html`
* Verified navigation renders correctly
* Verified parent index generation is idempotent
* Regenerated MCP docs and validated schema consistency

---

## Result

The documentation compiler now:

* Produces structurally correct static sites
* Supports flat and source-root modes
* Eliminates 403 root issues
* Scales cleanly across multiple repositories

This aligns doc-forge with proper static-site architectural invariants.

Reviewed-on: #4
Co-authored-by: Vishesh 'ironeagle' Bangotra <aetoskia@gmail.com>
Co-committed-by: Vishesh 'ironeagle' Bangotra <aetoskia@gmail.com>

.run/pytests.run.xml

@@ -1,5 +1,5 @@
 <component name="ProjectRunConfigurationManager">
-  <configuration default="false" name="pytest" type="tests" factoryName="py.test">
+  <configuration default="false" name="pytests" type="tests" factoryName="py.test">
     <module name="docforge" />
     <option name="ENV_FILES" value="" />
     <option name="INTERPRETER_OPTIONS" value="" />

docforge.nav.yml

@@ -1,26 +1,26 @@
-home: docforge/index.md
+home: index.md
 groups:
   Loaders:
-    - docforge/loaders/index.md
-    - docforge/loaders/griffe_loader.md
+    - loaders/index.md
+    - loaders/griffe_loader.md
   Models:
-    - docforge/models/index.md
-    - docforge/models/module.md
-    - docforge/models/object.md
-    - docforge/models/project.md
+    - models/index.md
+    - models/module.md
+    - models/object.md
+    - models/project.md
   Navigation:
-    - docforge/nav/index.md
-    - docforge/nav/spec.md
-    - docforge/nav/resolver.md
-    - docforge/nav/mkdocs.md
+    - nav/index.md
+    - nav/spec.md
+    - nav/resolver.md
+    - nav/mkdocs.md
   Renderers:
-    - docforge/renderers/index.md
-    - docforge/renderers/base.md
-    - docforge/renderers/mkdocs_renderer.md
-    - docforge/renderers/mcp_renderer.md
+    - renderers/index.md
+    - renderers/base.md
+    - renderers/mkdocs_renderer.md
+    - renderers/mcp_renderer.md
   CLI:
-    - docforge/cli/index.md
-    - docforge/cli/main.md
-    - docforge/cli/commands.md
-    - docforge/cli/mcp_utils.md
-    - docforge/cli/mkdocs_utils.md
+    - cli/index.md
+    - cli/main.md
+    - cli/commands.md
+    - cli/mcp_utils.md
+    - cli/mkdocs_utils.md

docforge/__init__.py

@@ -1,86 +1,208 @@
 """
-# doc-forge
+Renderer-agnostic Python documentation compiler that converts docstrings into
+structured documentation for both humans (MkDocs) and machines (MCP / AI agents).
 
-`doc-forge` is a renderer-agnostic Python documentation compiler designed for
-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.
+`doc-forge` statically analyzes your source code, builds a semantic model of
+modules and objects, and renders that model into documentation outputs without
+executing your code.
+
+---
 
 ## Core Philosophy
 
-`doc-forge` operates on two fundamental principles:
+`doc-forge` follows a compiler architecture:
 
-1.  **The Atomic Unit is a Python Import Path**: Documentation is organized around the semantic structure of your code (e.g., `mypackage.utils`), not the filesystem.
-2.  **The Documentation Compiler Paradigm**: We separate documentation into three distinct phases:
-    -   **Front-end (Introspection)**: Static analysis of source code and docstrings.
-    -   **Middle-end (Semantic Model)**: A renderer-neutral internal representation.
-    -   **Back-end (Renderers)**: Generation of human-facing (MkDocs) or machine-facing (MCP) outputs.
+1. **Front-end (Introspection)**
+   Static analysis of modules, classes, functions, signatures, and docstrings.
 
-## Documentation Design
+2. **Middle-end (Semantic Model)**
+   Renderer-neutral structured representation of your API.
 
-`doc-forge` is an "AI-Native" documentation compiler. To get the most out of it, design your docstrings with both humans and LLMs in mind:
+3. **Back-end (Renderers)**
 
-### For Humans (Readability & Structure)
-- **`__init__.py` as Landing Pages**: Use the docstring of your package's `__init__.py` as the home page. Include overviews, installation instructions, and high-level examples here.
-- **Single Source of Truth**: Keep all technical details in docstrings. This ensures your MkDocs/Sphinx sites stay in sync with the code.
-- **Semantic Hierarchy**: Use standard Markdown headers to structure complex module documentation.
+   * MkDocs → human documentation
+   * MCP JSON → AI-readable documentation
 
-### For LLMs (AI-Native Knowledge)
-- **Model Context Protocol (MCP)**: `doc-forge` exports your docs as structured JSON. This allows AI agents to "understand" your API surface area without layout noise.
-- **Canonical Paths**: Use dotted import paths as primary identifiers. AI tools use these to link code usage to documentation.
-- **Type Annotations**: While not in docstrings, `doc-forge` (via Griffe) extracts signatures. Clean type hints dramatically improve an LLM's ability to generate correct code using your library.
-## Available Commands
+The atomic unit of documentation is the Python import path.
 
-- **build**: Build documentation (MkDocs site or MCP resources).
-- **serve**: Serve documentation (MkDocs or MCP).
-- **tree**: Visualize the introspected project structure.
+Example:
+
+```python
+from my_package.foo import Bar
+```
+
+---
+
+## Docstring Writing Standard
+
+Docstrings are the single source of truth. `doc-forge` does not generate content.
+It compiles and renders what you write.
+
+Documentation follows the Python import hierarchy.
+
+---
+
+## Package docstring (`package/__init__.py`) — Full user guide
+
+This is the landing page. A developer must be able to install and use the
+package after reading only this docstring.
+
+Example:
+
+```python
+'''
+my_package
+
+Short description of what this package provides.
 
 ## Installation
 
-Install using `pip` with the optional `mkdocs` dependencies for a complete setup:
+pip install my-package
 
-```bash
-pip install doc-forge
+## Quick start
+
+from my_package.foo import Bar
+
+bar = Bar()
+result = bar.process("example")
+
+## Core concepts
+
+Bar
+    Primary object exposed by the package.
+
+foo module
+    Provides core functionality.
+
+## Typical workflow
+
+1. Import public objects
+2. Initialize objects
+3. Call methods
+
+## Public API
+
+foo.Bar
+foo.helper_function
+'''
 ```
 
-## Quick Start
+---
 
-1.  **Build Documentation**:
-    Introspect your package and generate documentation in one step:
-    ```bash
-    # Build MkDocs site
-    doc-forge build --mkdocs --module my_package --site-name "My Docs"
+## Submodule docstring (`package/foo/__init__.py`) — Subsystem guide
 
-    # Build MCP resources
-    doc-forge build --mcp --module my_package
-    ```
+Explains a specific subsystem.
 
-2.  **Define Navigation**:
-    Create a `docforge.nav.yml` to organize your documentation:
-    ```yaml
-    home: my_package/index.md
-    groups:
-      Core API:
-        - my_package/core/*.md
-      Utilities:
-        - my_package/utils.md
-    ```
+Example:
 
-3.  **Preview**:
-    ```bash
-    # Serve MkDocs site
-    doc-forge serve --mkdocs
+```python
+'''
+foo subsystem.
 
-    # Serve MCP documentation
-    doc-forge serve --mcp
-    ```
+Provides core functionality.
 
-## Project Structure
+## Usage
 
-- `docforge.loaders`: Introspects source code using static analysis (`griffe`).
-- `docforge.models`: The internal representation of your project, modules, and objects.
-- `docforge.renderers`: Converters that turn the models into physical files.
-- `docforge.nav`: Managers for logical-to-physical path mapping and navigation.
+from my_package.foo import Bar
+
+bar = Bar()
+bar.process("example")
+'''
+```
+
+---
+
+## Class docstring — Object contract
+
+Defines responsibility and behavior.
+
+Example:
+
+```python
+class Bar:
+    '''
+    Performs processing on input data.
+
+    Instances may be reused across multiple calls.
+    '''
+```
+
+Include:
+
+* Responsibility
+* Lifecycle expectations
+* Thread safety (if relevant)
+* Performance characteristics (if relevant)
+
+---
+
+## Function and method docstrings — API specification
+
+Example:
+
+```python
+def process(self, value: str) -> str:
+    '''
+    Process an input value.
+
+    Args:
+        value:
+            Input string.
+
+    Returns:
+        Processed string.
+
+    Raises:
+        ValueError:
+            If the input is invalid.
+    '''
+```
+
+---
+
+## Attribute docstrings (optional)
+
+Example:
+
+```python
+self.name: str
+'''Identifier used during processing.'''
+```
+
+---
+
+## Writing Rules
+
+**Required**
+
+* Use Markdown headings
+* Provide real import examples
+* Document all public APIs
+* Keep descriptions precise and factual
+
+**Avoid**
+
+* Plain-text separators like `====`
+* Duplicate external documentation
+* Informal or conversational language
+
+---
+
+## How doc-forge uses these docstrings
+
+Build MkDocs site:
+
+```bash
+doc-forge build --mkdocs --module my_package
+```
+
+Build MCP documentation:
+
+```bash
+doc-forge build --mcp --module my_package
+```
+
+Both outputs are generated directly from docstrings.
 """
 
 from .loaders import GriffeLoader, discover_module_paths

docforge/cli/commands.py

@@ -18,6 +18,7 @@ def cli() -> None:
 @cli.command()
 @click.option("--mcp", is_flag=True, help="Build MCP resources")
 @click.option("--mkdocs", is_flag=True, help="Build MkDocs site")
+@click.option("--module-is-source", is_flag=True, help="Module is source folder and to be treated as root folder")
 @click.option("--module", help="Python module to document")
 @click.option("--project-name", help="Project name override")
 # MkDocs specific
@@ -32,6 +33,7 @@ def cli() -> None:
 def build(
     mcp: bool,
     mkdocs: bool,
+    module_is_source: bool,
     module: Optional[str],
     project_name: Optional[str],
     site_name: Optional[str],
@@ -52,7 +54,8 @@ def build(
     Args:
         mcp: Use the MCP documentation builder.
         mkdocs: Use the MkDocs documentation builder.
-        module: The dotted path of the module to document.
+        module_is_source: Module is the source folder and to be treated as the root folder.
+        module: The dotted path of the module to the 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.
@@ -71,7 +74,12 @@ def build(
             site_name = module
 
         click.echo(f"Generating MkDocs sources in {docs_dir}...")
-        mkdocs_utils.generate_sources(module, project_name, docs_dir)
+        mkdocs_utils.generate_sources(
+            module,
+            docs_dir,
+            project_name,
+            module_is_source,
+        )
 
         click.echo(f"Generating MkDocs config {mkdocs_yml}...")
         mkdocs_utils.generate_config(docs_dir, nav_file, template, mkdocs_yml, site_name)

docforge/cli/commands.pyi

@@ -7,6 +7,7 @@ cli: Group
 def build(
     mcp: bool,
     mkdocs: bool,
+    module_is_source: bool,
     module: Optional[str],
     project_name: Optional[str],
     site_name: Optional[str],

docforge/cli/mkdocs_utils.py

@@ -6,7 +6,12 @@ from docforge.loaders import GriffeLoader, discover_module_paths
 from docforge.renderers import MkDocsRenderer
 from docforge.nav import load_nav_spec, resolve_nav, MkDocsNavEmitter
 
-def generate_sources(module: str, project_name: str | None, docs_dir: Path) -> None:
+def generate_sources(
+    module: str,
+    docs_dir: Path,
+    project_name: str | None = None,
+    module_is_source: bool | None = None,
+) -> None:
     """
     Generate Markdown source files for the specified module.
 
@@ -14,13 +19,18 @@ def generate_sources(module: str, project_name: str | None, docs_dir: Path) -> N
         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.
+        module_is_source: Module is the source folder and to be treated as the root folder.
     """
     loader = GriffeLoader()
     discovered_paths = discover_module_paths(module)
     project = loader.load_project(discovered_paths, project_name)
 
     renderer = MkDocsRenderer()
-    renderer.generate_sources(project, docs_dir)
+    renderer.generate_sources(
+        project,
+        docs_dir,
+        module_is_source,
+    )
 
 def generate_config(docs_dir: Path, nav_file: Path, template: Path | None, out: Path, site_name: str) -> None:
     """

docforge/cli/mkdocs_utils.pyi

@@ -1,6 +1,11 @@
 from pathlib import Path
 
-def generate_sources(module: str, project_name: str | None, docs_dir: Path) -> None: ...
+def generate_sources(
+    module: str,
+    docs_dir: Path,
+    project_name: str | None = None,
+    module_is_source: bool | None = None,
+) -> 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/mkdocs_renderer.py

@@ -1,11 +1,16 @@
 """
-This module implements the MkDocsRenderer, which generates Markdown source files
-compatible with the MkDocs 'material' theme and 'mkdocstrings' extension.
+MkDocsRenderer
+
+Generates Markdown source files compatible with MkDocs Material
+and mkdocstrings, ensuring:
+
+- Root index.md always exists
+- Parent package indexes are created automatically
+- Child modules are linked in parent index files
 """
 
 from pathlib import Path
-
-from docforge.models import Project
+from docforge.models import Project, Module
 
 
 class MkDocsRenderer:
@@ -16,7 +21,15 @@ class MkDocsRenderer:
 
     name = "mkdocs"
 
-    def generate_sources(self, project: Project, out_dir: Path) -> None:
+    # -------------------------
+    # Public API
+    # -------------------------
+    def generate_sources(
+        self,
+        project: Project,
+        out_dir: Path,
+        module_is_source: bool | None = None,
+    ) -> None:
         """
         Produce a set of Markdown files in the output directory based on the
         provided Project models.
@@ -24,7 +37,11 @@ class MkDocsRenderer:
         Args:
             project: The project models to render.
             out_dir: Target directory for documentation files.
+            module_is_source: Module is the source folder and to be treated as the root folder.
         """
+        out_dir.mkdir(parents=True, exist_ok=True)
+        self._ensure_root_index(project, out_dir)
+
         modules = list(project.get_all_modules())
         paths = {m.path for m in modules}
 
@@ -35,12 +52,23 @@ class MkDocsRenderer:
         }
 
         for module in modules:
-            self._write_module(module, packages, out_dir)
+            self._write_module(
+                module,
+                packages,
+                out_dir,
+                module_is_source,
+            )
 
     # -------------------------
     # Internal helpers
     # -------------------------
-    def _write_module(self, module, packages: set[str], out_dir: Path) -> None:
+    def _write_module(
+        self,
+        module: Module,
+        packages: set[str],
+        out_dir: Path,
+        module_is_source: bool | None = None,
+    ) -> None:
         """
         Write a single module's documentation file. Packages are written as
         'index.md' inside their respective directories.
@@ -49,31 +77,37 @@ class MkDocsRenderer:
             module: The module to write.
             packages: A set of module paths that are identified as packages.
             out_dir: The base output directory.
+            module_is_source: Module is the source folder and to be treated as the root folder.
         """
         parts = module.path.split(".")
 
+        if module_is_source:
+            module_name, parts = parts[0], parts[1:]
+        else:
+            module_name, parts = parts[0], parts
+
         if module.path in packages:
-            # package → index.md
+            # Package → directory/index.md
             dir_path = out_dir.joinpath(*parts)
             dir_path.mkdir(parents=True, exist_ok=True)
-
             md_path = dir_path / "index.md"
-            title = parts[-1].replace("_", " ").title()
+            link_target = f"{parts[-1]}/" if parts else None
         else:
-            # leaf module → <name>.md
+            # Leaf module → parent_dir/<name>.md
             dir_path = out_dir.joinpath(*parts[:-1])
             dir_path.mkdir(parents=True, exist_ok=True)
-
             md_path = dir_path / f"{parts[-1]}.md"
-            title = parts[-1].replace("_", " ").title()
+            link_target = f"{parts[-1]}.md" if parts else None
 
+        title = parts[-1].replace("_", " ").title() if parts else module_name
         content = self._render_markdown(title, module.path)
 
-        if md_path.exists() and md_path.read_text(encoding="utf-8") == content:
-            return
-
+        if not md_path.exists() or md_path.read_text(encoding="utf-8") != content:
             md_path.write_text(content, encoding="utf-8")
 
+        if not module_is_source:
+            self._ensure_parent_index(parts, out_dir, link_target, title)
+
     def _render_markdown(self, title: str, module_path: str) -> str:
         """
         Generate the Markdown content for a module file.
@@ -89,3 +123,46 @@ class MkDocsRenderer:
             f"# {title}\n\n"
             f"::: {module_path}\n"
         )
+
+    def _ensure_root_index(
+        self,
+        project: Project,
+        out_dir: Path
+    ) -> None:
+        root_index = out_dir / "index.md"
+
+        if not root_index.exists():
+            root_index.write_text(
+                f"# {project.name}\n\n"
+                "## Modules\n\n",
+                encoding="utf-8",
+            )
+
+    def _ensure_parent_index(
+        self,
+        parts: list[str],
+        out_dir: Path,
+        link_target: str,
+        title: str,
+    ) -> None:
+        if len(parts) == 1:
+            parent_index = out_dir / "index.md"
+            link = f"- [{title}]({link_target})\n"
+        else:
+            parent_dir = out_dir.joinpath(*parts[:-1])
+            parent_dir.mkdir(parents=True, exist_ok=True)
+            parent_index = parent_dir / "index.md"
+
+            link = f"- [{title}]({link_target})\n"
+
+            if not parent_index.exists():
+                parent_title = parts[-2].replace("_", " ").title()
+                parent_index.write_text(
+                    f"# {parent_title}\n\n",
+                    encoding="utf-8",
+                )
+
+        content = parent_index.read_text(encoding="utf-8")
+
+        if link not in content:
+            parent_index.write_text(content + link, encoding="utf-8")

docforge/renderers/mkdocs_renderer.pyi

@@ -1,17 +1,27 @@
 from pathlib import Path
-from typing import Set
-
 from docforge.models import Project, Module
 
 
 class MkDocsRenderer:
     name: str
 
-    def generate_sources(self, project: Project, out_dir: Path) -> None: ...
+    def generate_sources(
+        self,
+        project: Project,
+        out_dir: Path,
+        module_is_source: bool | None = None,
+    ) -> None: ...
+
     def _write_module(
         self,
         module: Module,
-        packages: Set[str],
+        packages: set[str],
         out_dir: Path,
+        module_is_source: bool | None = None,
     ) -> None: ...
+
     def _render_markdown(self, title: str, module_path: str) -> str: ...
+
+    def _ensure_root_index(self, project, out_dir) -> None: ...
+
+    def _ensure_parent_index(self, parts, out_dir, link_target, title) -> None: ...

docs/index.md

@@ -1,3 +1,3 @@
-# Docforge
+# docforge
 
 ::: docforge

mcp_docs/modules/docforge.cli.commands.json

@@ -139,7 +139,7 @@
                 "kind": "function",
                 "path": "docforge.cli.commands.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."
+                "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.\n    module_is_source: Module is the source folder and to be treated as the root folder."
               }
             }
           },
@@ -178,7 +178,7 @@
             "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."
+            "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.\n    module_is_source: Module is the source folder and to be treated as the root folder."
           },
           "generate_config": {
             "name": "generate_config",
@@ -319,7 +319,7 @@
             "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/."
+            "docstring": "Serve MCP documentation from a pre-built bundle.\n\nArgs:\n    module: The dotted path of the primary module to serve.\n    mcp_root: Path to the directory containing index.json, nav.json, and modules/."
           }
         }
       },
@@ -334,22 +334,22 @@
         "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', 18, 97)>",
+        "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_is_source: Module is the source folder and to be treated as the root folder.\n    module: The dotted path of the module to the 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."
       },
       "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', 100, 133)>",
+        "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    module: The dotted path of the module to serve.\n    mkdocs_yml: (MkDocs) Path to the mkdocs.yml configuration.\n    out_dir: (MCP) Path to the mcp_docs/ directory."
       },
       "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."
+        "signature": "<bound method Function.signature of Function('tree', 136, 165)>",
+        "docstring": "Visualize the project structure in the terminal.\n\nArgs:\n    module: The module import path to recursively introspect.\n    project_name: Optional override for the project name shown at the root."
       },
       "Group": {
         "name": "Group",

mcp_docs/modules/docforge.cli.json

@@ -169,7 +169,7 @@
                     "kind": "function",
                     "path": "docforge.cli.commands.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."
+                    "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.\n    module_is_source: Module is the source folder and to be treated as the root folder."
                   }
                 }
               },
@@ -208,7 +208,7 @@
                 "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."
+                "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.\n    module_is_source: Module is the source folder and to be treated as the root folder."
               },
               "generate_config": {
                 "name": "generate_config",
@@ -349,7 +349,7 @@
                 "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/."
+                "docstring": "Serve MCP documentation from a pre-built bundle.\n\nArgs:\n    module: The dotted path of the primary module to serve.\n    mcp_root: Path to the directory containing index.json, nav.json, and modules/."
               }
             }
           },
@@ -364,22 +364,22 @@
             "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', 18, 97)>",
+            "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_is_source: Module is the source folder and to be treated as the root folder.\n    module: The dotted path of the module to the 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."
           },
           "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', 100, 133)>",
+            "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    module: The dotted path of the module to serve.\n    mkdocs_yml: (MkDocs) Path to the mkdocs.yml configuration.\n    out_dir: (MCP) Path to the mcp_docs/ directory."
           },
           "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."
+            "signature": "<bound method Function.signature of Function('tree', 136, 165)>",
+            "docstring": "Visualize the project structure in the terminal.\n\nArgs:\n    module: The module import path to recursively introspect.\n    project_name: Optional override for the project name shown at the root."
           },
           "Group": {
             "name": "Group",
@@ -512,8 +512,8 @@
             "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/."
+            "signature": "<bound method Function.signature of Function('serve', 23, 48)>",
+            "docstring": "Serve MCP documentation from a pre-built bundle.\n\nArgs:\n    module: The dotted path of the primary module to serve.\n    mcp_root: Path to the directory containing index.json, nav.json, and modules/."
           }
         }
       },
@@ -601,7 +601,7 @@
                 "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."
+                "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.\n    module_is_source: Module is the source folder and to be treated as the root folder."
               }
             }
           },
@@ -639,28 +639,28 @@
             "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."
+            "signature": "<bound method Function.signature of Function('generate_sources', 9, 33)>",
+            "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.\n    module_is_source: Module is the source folder and to be treated as the root folder."
           },
           "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)>",
+            "signature": "<bound method Function.signature of Function('generate_config', 35, 69)>",
             "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)>",
+            "signature": "<bound method Function.signature of Function('build', 71, 84)>",
             "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)>",
+            "signature": "<bound method Function.signature of Function('serve', 86, 97)>",
             "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.mcp_utils.json

@@ -112,8 +112,8 @@
         "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/."
+        "signature": "<bound method Function.signature of Function('serve', 23, 48)>",
+        "docstring": "Serve MCP documentation from a pre-built bundle.\n\nArgs:\n    module: The dotted path of the primary module to serve.\n    mcp_root: Path to the directory containing index.json, nav.json, and modules/."
       }
     }
   }

mcp_docs/modules/docforge.cli.mkdocs_utils.json

@@ -81,7 +81,7 @@
             "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."
+            "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.\n    module_is_source: Module is the source folder and to be treated as the root folder."
           }
         }
       },
@@ -119,28 +119,28 @@
         "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."
+        "signature": "<bound method Function.signature of Function('generate_sources', 9, 33)>",
+        "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.\n    module_is_source: Module is the source folder and to be treated as the root folder."
       },
       "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)>",
+        "signature": "<bound method Function.signature of Function('generate_config', 35, 69)>",
         "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)>",
+        "signature": "<bound method Function.signature of Function('build', 71, 84)>",
         "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)>",
+        "signature": "<bound method Function.signature of Function('serve', 86, 97)>",
         "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.json

@@ -2,7 +2,7 @@
   "module": "docforge",
   "content": {
     "path": "docforge",
-    "docstring": "# doc-forge\n\n`doc-forge` is a renderer-agnostic Python documentation compiler designed for\nspeed, flexibility, and beautiful output. It decouples the introspection of\nyour code from the rendering process, allowing you to generate documentation\nfor various platforms (starting with MkDocs) from a single internal models.\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.\n\n## Installation\n\nInstall using `pip` with the optional `mkdocs` dependencies for a complete setup:\n\n```bash\npip install doc-forge\n```\n\n## Quick Start\n\n1.  **Build Documentation**:\n    Introspect your package and generate documentation in one step:\n    ```bash\n    # Build MkDocs site\n    doc-forge build --mkdocs --module my_package --site-name \"My Docs\"\n\n    # Build MCP resources\n    doc-forge build --mcp --module my_package\n    ```\n\n2.  **Define Navigation**:\n    Create a `docforge.nav.yml` to organize your documentation:\n    ```yaml\n    home: my_package/index.md\n    groups:\n      Core API:\n        - my_package/core/*.md\n      Utilities:\n        - my_package/utils.md\n    ```\n\n3.  **Preview**:\n    ```bash\n    # Serve MkDocs site\n    doc-forge serve --mkdocs\n\n    # Serve MCP documentation\n    doc-forge serve --mcp\n    ```\n\n## Project Structure\n\n- `docforge.loaders`: Introspects source code using static analysis (`griffe`).\n- `docforge.models`: The internal representation of your project, modules, and objects.\n- `docforge.renderers`: Converters that turn the models into physical files.\n- `docforge.nav`: Managers for logical-to-physical path mapping and navigation.",
+    "docstring": "Renderer-agnostic Python documentation compiler that converts docstrings into\nstructured documentation for both humans (MkDocs) and machines (MCP / AI agents).\n\n`doc-forge` statically analyzes your source code, builds a semantic model of\nmodules and objects, and renders that model into documentation outputs without\nexecuting your code.\n\n---\n\n## Core Philosophy\n\n`doc-forge` follows a compiler architecture:\n\n1. **Front-end (Introspection)**\n   Static analysis of modules, classes, functions, signatures, and docstrings.\n\n2. **Middle-end (Semantic Model)**\n   Renderer-neutral structured representation of your API.\n\n3. **Back-end (Renderers)**\n\n   * MkDocs → human documentation\n   * MCP JSON → AI-readable documentation\n\nThe atomic unit of documentation is the Python import path.\n\nExample:\n\n```python\nfrom my_package.foo import Bar\n```\n\n---\n\n## Docstring Writing Standard\n\nDocstrings are the single source of truth. `doc-forge` does not generate content.\nIt compiles and renders what you write.\n\nDocumentation follows the Python import hierarchy.\n\n---\n\n## Package docstring (`package/__init__.py`) — Full user guide\n\nThis is the landing page. A developer must be able to install and use the\npackage after reading only this docstring.\n\nExample:\n\n```python\n'''\nmy_package\n\nShort description of what this package provides.\n\n## Installation\n\npip install my-package\n\n## Quick start\n\nfrom my_package.foo import Bar\n\nbar = Bar()\nresult = bar.process(\"example\")\n\n## Core concepts\n\nBar\n    Primary object exposed by the package.\n\nfoo module\n    Provides core functionality.\n\n## Typical workflow\n\n1. Import public objects\n2. Initialize objects\n3. Call methods\n\n## Public API\n\nfoo.Bar\nfoo.helper_function\n'''\n```\n\n---\n\n## Submodule docstring (`package/foo/__init__.py`) — Subsystem guide\n\nExplains a specific subsystem.\n\nExample:\n\n```python\n'''\nfoo subsystem.\n\nProvides core functionality.\n\n## Usage\n\nfrom my_package.foo import Bar\n\nbar = Bar()\nbar.process(\"example\")\n'''\n```\n\n---\n\n## Class docstring — Object contract\n\nDefines responsibility and behavior.\n\nExample:\n\n```python\nclass Bar:\n    '''\n    Performs processing on input data.\n\n    Instances may be reused across multiple calls.\n    '''\n```\n\nInclude:\n\n* Responsibility\n* Lifecycle expectations\n* Thread safety (if relevant)\n* Performance characteristics (if relevant)\n\n---\n\n## Function and method docstrings — API specification\n\nExample:\n\n```python\ndef process(self, value: str) -> str:\n    '''\n    Process an input value.\n\n    Args:\n        value:\n            Input string.\n\n    Returns:\n        Processed string.\n\n    Raises:\n        ValueError:\n            If the input is invalid.\n    '''\n```\n\n---\n\n## Attribute docstrings (optional)\n\nExample:\n\n```python\nself.name: str\n'''Identifier used during processing.'''\n```\n\n---\n\n## Writing Rules\n\n**Required**\n\n* Use Markdown headings\n* Provide real import examples\n* Document all public APIs\n* Keep descriptions precise and factual\n\n**Avoid**\n\n* Plain-text separators like `====`\n* Duplicate external documentation\n* Informal or conversational language\n\n---\n\n## How doc-forge uses these docstrings\n\nBuild MkDocs site:\n\n```bash\ndoc-forge build --mkdocs --module my_package\n```\n\nBuild MCP documentation:\n\n```bash\ndoc-forge build --mcp --module my_package\n```\n\nBoth outputs are generated directly from docstrings.",
     "objects": {
       "GriffeLoader": {
         "name": "GriffeLoader",
@@ -53,7 +53,7 @@
             "kind": "function",
             "path": "docforge.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."
+            "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.\n    module_is_source: Module is the source folder and to be treated as the root folder."
           }
         }
       },
@@ -275,7 +275,7 @@
                         "kind": "function",
                         "path": "docforge.cli.commands.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."
+                        "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.\n    module_is_source: Module is the source folder and to be treated as the root folder."
                       }
                     }
                   },
@@ -314,7 +314,7 @@
                     "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."
+                    "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.\n    module_is_source: Module is the source folder and to be treated as the root folder."
                   },
                   "generate_config": {
                     "name": "generate_config",
@@ -455,7 +455,7 @@
                     "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/."
+                    "docstring": "Serve MCP documentation from a pre-built bundle.\n\nArgs:\n    module: The dotted path of the primary module to serve.\n    mcp_root: Path to the directory containing index.json, nav.json, and modules/."
                   }
                 }
               },
@@ -470,22 +470,22 @@
                 "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', 18, 97)>",
+                "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_is_source: Module is the source folder and to be treated as the root folder.\n    module: The dotted path of the module to the 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."
               },
               "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', 100, 133)>",
+                "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    module: The dotted path of the module to serve.\n    mkdocs_yml: (MkDocs) Path to the mkdocs.yml configuration.\n    out_dir: (MCP) Path to the mcp_docs/ directory."
               },
               "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."
+                "signature": "<bound method Function.signature of Function('tree', 136, 165)>",
+                "docstring": "Visualize the project structure in the terminal.\n\nArgs:\n    module: The module import path to recursively introspect.\n    project_name: Optional override for the project name shown at the root."
               },
               "Group": {
                 "name": "Group",
@@ -618,8 +618,8 @@
                 "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/."
+                "signature": "<bound method Function.signature of Function('serve', 23, 48)>",
+                "docstring": "Serve MCP documentation from a pre-built bundle.\n\nArgs:\n    module: The dotted path of the primary module to serve.\n    mcp_root: Path to the directory containing index.json, nav.json, and modules/."
               }
             }
           },
@@ -707,7 +707,7 @@
                     "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."
+                    "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.\n    module_is_source: Module is the source folder and to be treated as the root folder."
                   }
                 }
               },
@@ -745,28 +745,28 @@
                 "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."
+                "signature": "<bound method Function.signature of Function('generate_sources', 9, 33)>",
+                "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.\n    module_is_source: Module is the source folder and to be treated as the root folder."
               },
               "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)>",
+                "signature": "<bound method Function.signature of Function('generate_config', 35, 69)>",
                 "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)>",
+                "signature": "<bound method Function.signature of Function('build', 71, 84)>",
                 "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)>",
+                "signature": "<bound method Function.signature of Function('serve', 86, 97)>",
                 "docstring": "Serve the documentation site with live-reload using MkDocs.\n\nArgs:\n    mkdocs_yml: Path to the mkdocs.yml configuration file."
               }
             }
@@ -2079,7 +2079,7 @@
                 "kind": "function",
                 "path": "docforge.renderers.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."
+                "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.\n    module_is_source: Module is the source folder and to be treated as the root folder."
               }
             }
           },
@@ -2465,7 +2465,7 @@
             "kind": "module",
             "path": "docforge.renderers.mkdocs_renderer",
             "signature": null,
-            "docstring": "This module implements the MkDocsRenderer, which generates Markdown source files\ncompatible with the MkDocs 'material' theme and 'mkdocstrings' extension.",
+            "docstring": "MkDocsRenderer\n\nGenerates Markdown source files compatible with MkDocs Material\nand mkdocstrings, ensuring:\n\n- Root index.md always exists\n- Parent package indexes are created automatically\n- Child modules are linked in parent index files",
             "members": {
               "Path": {
                 "name": "Path",
@@ -2525,36 +2525,6 @@
                   }
                 }
               },
-              "MkDocsRenderer": {
-                "name": "MkDocsRenderer",
-                "kind": "class",
-                "path": "docforge.renderers.mkdocs_renderer.MkDocsRenderer",
-                "signature": "<bound method Class.signature of Class('MkDocsRenderer', 11, 91)>",
-                "docstring": "Renderer that generates Markdown source files formatted for the MkDocs\n'mkdocstrings' plugin.",
-                "members": {
-                  "name": {
-                    "name": "name",
-                    "kind": "attribute",
-                    "path": "docforge.renderers.mkdocs_renderer.MkDocsRenderer.name",
-                    "signature": null,
-                    "docstring": null
-                  },
-                  "generate_sources": {
-                    "name": "generate_sources",
-                    "kind": "function",
-                    "path": "docforge.renderers.mkdocs_renderer.MkDocsRenderer.generate_sources",
-                    "signature": "<bound method Function.signature of Function('generate_sources', 19, 38)>",
-                    "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."
-                  }
-                }
-              },
-              "Set": {
-                "name": "Set",
-                "kind": "alias",
-                "path": "docforge.renderers.mkdocs_renderer.Set",
-                "signature": "<bound method Alias.signature of Alias('Set', 'typing.Set')>",
-                "docstring": null
-              },
               "Module": {
                 "name": "Module",
                 "kind": "class",
@@ -2605,6 +2575,29 @@
                     "docstring": "Get all top-level objects in the module.\n\nReturns:\n    An iterable of DocObject instances."
                   }
                 }
+              },
+              "MkDocsRenderer": {
+                "name": "MkDocsRenderer",
+                "kind": "class",
+                "path": "docforge.renderers.mkdocs_renderer.MkDocsRenderer",
+                "signature": "<bound method Class.signature of Class('MkDocsRenderer', 16, 168)>",
+                "docstring": "Renderer that generates Markdown source files formatted for the MkDocs\n'mkdocstrings' plugin.",
+                "members": {
+                  "name": {
+                    "name": "name",
+                    "kind": "attribute",
+                    "path": "docforge.renderers.mkdocs_renderer.MkDocsRenderer.name",
+                    "signature": null,
+                    "docstring": null
+                  },
+                  "generate_sources": {
+                    "name": "generate_sources",
+                    "kind": "function",
+                    "path": "docforge.renderers.mkdocs_renderer.MkDocsRenderer.generate_sources",
+                    "signature": "<bound method Function.signature of Function('generate_sources', 27, 60)>",
+                    "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.\n    module_is_source: Module is the source folder and to be treated as the root folder."
+                  }
+                }
               }
             }
           }

mcp_docs/modules/docforge.renderers.json

@@ -23,7 +23,7 @@
             "kind": "function",
             "path": "docforge.renderers.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."
+            "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.\n    module_is_source: Module is the source folder and to be treated as the root folder."
           }
         }
       },
@@ -409,7 +409,7 @@
         "kind": "module",
         "path": "docforge.renderers.mkdocs_renderer",
         "signature": null,
-        "docstring": "This module implements the MkDocsRenderer, which generates Markdown source files\ncompatible with the MkDocs 'material' theme and 'mkdocstrings' extension.",
+        "docstring": "MkDocsRenderer\n\nGenerates Markdown source files compatible with MkDocs Material\nand mkdocstrings, ensuring:\n\n- Root index.md always exists\n- Parent package indexes are created automatically\n- Child modules are linked in parent index files",
         "members": {
           "Path": {
             "name": "Path",
@@ -469,36 +469,6 @@
               }
             }
           },
-          "MkDocsRenderer": {
-            "name": "MkDocsRenderer",
-            "kind": "class",
-            "path": "docforge.renderers.mkdocs_renderer.MkDocsRenderer",
-            "signature": "<bound method Class.signature of Class('MkDocsRenderer', 11, 91)>",
-            "docstring": "Renderer that generates Markdown source files formatted for the MkDocs\n'mkdocstrings' plugin.",
-            "members": {
-              "name": {
-                "name": "name",
-                "kind": "attribute",
-                "path": "docforge.renderers.mkdocs_renderer.MkDocsRenderer.name",
-                "signature": null,
-                "docstring": null
-              },
-              "generate_sources": {
-                "name": "generate_sources",
-                "kind": "function",
-                "path": "docforge.renderers.mkdocs_renderer.MkDocsRenderer.generate_sources",
-                "signature": "<bound method Function.signature of Function('generate_sources', 19, 38)>",
-                "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."
-              }
-            }
-          },
-          "Set": {
-            "name": "Set",
-            "kind": "alias",
-            "path": "docforge.renderers.mkdocs_renderer.Set",
-            "signature": "<bound method Alias.signature of Alias('Set', 'typing.Set')>",
-            "docstring": null
-          },
           "Module": {
             "name": "Module",
             "kind": "class",
@@ -549,6 +519,29 @@
                 "docstring": "Get all top-level objects in the module.\n\nReturns:\n    An iterable of DocObject instances."
               }
             }
+          },
+          "MkDocsRenderer": {
+            "name": "MkDocsRenderer",
+            "kind": "class",
+            "path": "docforge.renderers.mkdocs_renderer.MkDocsRenderer",
+            "signature": "<bound method Class.signature of Class('MkDocsRenderer', 16, 168)>",
+            "docstring": "Renderer that generates Markdown source files formatted for the MkDocs\n'mkdocstrings' plugin.",
+            "members": {
+              "name": {
+                "name": "name",
+                "kind": "attribute",
+                "path": "docforge.renderers.mkdocs_renderer.MkDocsRenderer.name",
+                "signature": null,
+                "docstring": null
+              },
+              "generate_sources": {
+                "name": "generate_sources",
+                "kind": "function",
+                "path": "docforge.renderers.mkdocs_renderer.MkDocsRenderer.generate_sources",
+                "signature": "<bound method Function.signature of Function('generate_sources', 27, 60)>",
+                "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.\n    module_is_source: Module is the source folder and to be treated as the root folder."
+              }
+            }
           }
         }
       }

mcp_docs/modules/docforge.renderers.mkdocs_renderer.json

@@ -2,7 +2,7 @@
   "module": "docforge.renderers.mkdocs_renderer",
   "content": {
     "path": "docforge.renderers.mkdocs_renderer",
-    "docstring": "This module implements the MkDocsRenderer, which generates Markdown source files\ncompatible with the MkDocs 'material' theme and 'mkdocstrings' extension.",
+    "docstring": "MkDocsRenderer\n\nGenerates Markdown source files compatible with MkDocs Material\nand mkdocstrings, ensuring:\n\n- Root index.md always exists\n- Parent package indexes are created automatically\n- Child modules are linked in parent index files",
     "objects": {
       "Path": {
         "name": "Path",
@@ -62,36 +62,6 @@
           }
         }
       },
-      "MkDocsRenderer": {
-        "name": "MkDocsRenderer",
-        "kind": "class",
-        "path": "docforge.renderers.mkdocs_renderer.MkDocsRenderer",
-        "signature": "<bound method Class.signature of Class('MkDocsRenderer', 11, 91)>",
-        "docstring": "Renderer that generates Markdown source files formatted for the MkDocs\n'mkdocstrings' plugin.",
-        "members": {
-          "name": {
-            "name": "name",
-            "kind": "attribute",
-            "path": "docforge.renderers.mkdocs_renderer.MkDocsRenderer.name",
-            "signature": null,
-            "docstring": null
-          },
-          "generate_sources": {
-            "name": "generate_sources",
-            "kind": "function",
-            "path": "docforge.renderers.mkdocs_renderer.MkDocsRenderer.generate_sources",
-            "signature": "<bound method Function.signature of Function('generate_sources', 19, 38)>",
-            "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."
-          }
-        }
-      },
-      "Set": {
-        "name": "Set",
-        "kind": "alias",
-        "path": "docforge.renderers.mkdocs_renderer.Set",
-        "signature": "<bound method Alias.signature of Alias('Set', 'typing.Set')>",
-        "docstring": null
-      },
       "Module": {
         "name": "Module",
         "kind": "class",
@@ -142,6 +112,29 @@
             "docstring": "Get all top-level objects in the module.\n\nReturns:\n    An iterable of DocObject instances."
           }
         }
+      },
+      "MkDocsRenderer": {
+        "name": "MkDocsRenderer",
+        "kind": "class",
+        "path": "docforge.renderers.mkdocs_renderer.MkDocsRenderer",
+        "signature": "<bound method Class.signature of Class('MkDocsRenderer', 16, 168)>",
+        "docstring": "Renderer that generates Markdown source files formatted for the MkDocs\n'mkdocstrings' plugin.",
+        "members": {
+          "name": {
+            "name": "name",
+            "kind": "attribute",
+            "path": "docforge.renderers.mkdocs_renderer.MkDocsRenderer.name",
+            "signature": null,
+            "docstring": null
+          },
+          "generate_sources": {
+            "name": "generate_sources",
+            "kind": "function",
+            "path": "docforge.renderers.mkdocs_renderer.MkDocsRenderer.generate_sources",
+            "signature": "<bound method Function.signature of Function('generate_sources', 27, 60)>",
+            "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.\n    module_is_source: Module is the source folder and to be treated as the root folder."
+          }
+        }
       }
     }
   }

mkdocs.yml

@@ -1,5 +1,3 @@
-site_name: docforge
-
 theme:
   name: material
   palette:
@@ -33,30 +31,30 @@ plugins:
           annotations_path: brief
           show_root_heading: true
           group_by_category: true
-
+site_name: docforge
 nav:
-- Home: docforge/index.md
+- Home: index.md
 - Loaders:
-  - docforge/loaders/index.md
-  - docforge/loaders/griffe_loader.md
+  - loaders/index.md
+  - loaders/griffe_loader.md
 - Models:
-  - docforge/models/index.md
-  - docforge/models/module.md
-  - docforge/models/object.md
-  - docforge/models/project.md
+  - models/index.md
+  - models/module.md
+  - models/object.md
+  - models/project.md
 - Navigation:
-  - docforge/nav/index.md
-  - docforge/nav/spec.md
-  - docforge/nav/resolver.md
-  - docforge/nav/mkdocs.md
+  - nav/index.md
+  - nav/spec.md
+  - nav/resolver.md
+  - nav/mkdocs.md
 - Renderers:
-  - docforge/renderers/index.md
-  - docforge/renderers/base.md
-  - docforge/renderers/mkdocs_renderer.md
-  - docforge/renderers/mcp_renderer.md
+  - renderers/index.md
+  - renderers/base.md
+  - renderers/mkdocs_renderer.md
+  - renderers/mcp_renderer.md
 - CLI:
-  - docforge/cli/index.md
-  - docforge/cli/main.md
-  - docforge/cli/commands.md
-  - docforge/cli/mcp_utils.md
-  - docforge/cli/mkdocs_utils.md
+  - cli/index.md
+  - cli/main.md
+  - cli/commands.md
+  - cli/mcp_utils.md
+  - cli/mkdocs_utils.md

pyproject.toml

@@ -5,7 +5,7 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "doc-forge"
-version = "0.0.4"
+version = "0.0.5"
 description = "A renderer-agnostic Python documentation compiler"
 readme = "README.md"
 requires-python = ">=3.10"