Flatten MkDocs Structure + --module-is-source Support (#4)

# 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>

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:
     """