- Consolidated CLI commands into [build](cci:1://file:///c:/Users/vishe/WorkSpace/code/aetos/doc-forge/docforge/cli/mkdocs/logic.py:48:0-58:46) and [serve](cci:1://file:///c:/Users/vishe/WorkSpace/code/aetos/doc-forge/docforge/cli/commands.py:70:0-92:32) using `--mkdocs` and `--mcp` flags.
- Separated CLI orchestration logic into [docforge/cli/mkdocs/logic.py](cci:7://file:///c:/Users/vishe/WorkSpace/code/aetos/doc-forge/docforge/cli/mkdocs/logic.py:0:0-0:0) and [docforge/cli/mcp/logic.py](cci:7://file:///c:/Users/vishe/WorkSpace/code/aetos/doc-forge/docforge/cli/mcp/logic.py:0:0-0:0).
- Moved command definitions to [docforge/cli/commands.py](cci:7://file:///c:/Users/vishe/WorkSpace/code/aetos/doc-forge/docforge/cli/commands.py:0:0-0:0), making [main.py](cci:7://file:///c:/Users/vishe/WorkSpace/code/aetos/doc-forge/docforge/cli/main.py:0:0-0:0) a thin entry point.
- Aligned [.pyi](cci:7://file:///c:/Users/vishe/WorkSpace/code/aetos/doc-forge/docforge/cli/main.pyi:0:0-0:0) type stubs with [.py](cci:7://file:///c:/Users/vishe/WorkSpace/code/aetos/doc-forge/tests/conftest.py:0:0-0:0) implementations across the package.
- Added missing docstrings to internal helper functions and core classes.
- Restructured tests into `tests/mkdocs/` and `tests/mcp/`.
- Updated navigation specification to reflect the new project structure.
- Add MCPRenderer to generate MCP-native JSON bundles (index.json, nav.json, modules/*.json)
- Expose MCPRenderer via public API and CLI (`generate-mcp` command)
- Replace Markdown-based MCP output with structured JSON resources
- Update MCP renderer type stubs to match new JSON-based implementation
- Refactor MCP tests to validate JSON content, bundle structure, and navigation
- Fix MCP module coverage test to use explicit project_root for reliable discovery
