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/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)