fix: make MkDocs generation filesystem-complete and package-aware

- Add filesystem-based module discovery via `discover_module_paths`
- Decouple documentation coverage from Python import behavior
- Ensure GriffeLoader receives a full module list instead of a single root
- Make MkDocs renderer level-agnostic using global package detection
- Emit `index.md` only for true packages, suppress `<package>.md`
- Mirror full dotted module hierarchy into nested docs directories
- Update CLI, exports, and type stubs to expose discovery helper
- Align tests with filesystem-driven module coverage

This fixes missing docs for submodules and removes invalid package `.md` files.

docforge/renderers/mkdocs.pyi

@@ -1,17 +1,17 @@
 from pathlib import Path
+from typing import Set
 
-from docforge.model import Project
-from docforge.renderers.base import DocRenderer
+from docforge.model import Project, Module
 
 
 class MkDocsRenderer:
-    """MkDocs source generator using mkdocstrings."""
-
     name: str
 
-    def generate_sources(
+    def generate_sources(self, project: Project, out_dir: Path) -> None: ...
+    def _write_module(
         self,
-        project: Project,
+        module: Module,
+        packages: Set[str],
         out_dir: Path,
-    ) -> None:
-        """Generate Markdown files with mkdocstrings directives."""
+    ) -> None: ...
+    def _render_markdown(self, title: str, module_path: str) -> str: ...