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/cli/main.py

@@ -5,7 +5,7 @@ from typing import Sequence, Optional
 
 import click
 
-from docforge.loader import GriffeLoader
+from docforge.loader import GriffeLoader, discover_module_paths
 from docforge.renderers.mkdocs import MkDocsRenderer
 from docforge.cli.mkdocs import mkdocs_cmd
 
@@ -83,7 +83,14 @@ def generate(
 ) -> None:
     """Generate documentation source files using MkDocs renderer."""
     loader = GriffeLoader()
-    project = loader.load_project(list(modules), project_name)
+    discovered_paths = discover_module_paths(
+        "docforge",
+        Path(r"C:\Users\vishe\WorkSpace\code\aetos\doc-forge")
+    )
+    project = loader.load_project(
+        discovered_paths,
+        project_name
+    )
 
     renderer = MkDocsRenderer()
     renderer.generate_sources(project, docs_dir)