feat: MCP server refactor with fine-grained tools and incremental update support

.gitignore

@@ -72,3 +72,4 @@ Thumbs.db
 *.tmp
 *.log
 *.bak
+.codewiki/

codewiki/__init__.py

@@ -1,14 +1,13 @@
 """
 CodeWiki: Transform codebases into comprehensive documentation using AI-powered analysis.
 
-This package provides a CLI tool for generating documentation from code repositories.
+This package provides a CLI tool for generating documentation from code repositories,
+and an MCP server for IDE-driven documentation generation.
 """
 
 __version__ = "1.0.1"
 __author__ = "CodeWiki Contributors"
 __license__ = "MIT"
 
-from codewiki.cli.main import cli
-
-__all__ = ["cli", "__version__"]
+__all__ = ["__version__"]
 

codewiki/cli/adapters/doc_generator.py

@@ -37,7 +37,8 @@ def __init__(
         output_dir: Path,
         config: Dict[str, Any],
         verbose: bool = False,
-        generate_html: bool = False
+        generate_html: bool = False,
+        commit_id: str = None,
     ):
         """
         Initialize the CLI documentation generator.
@@ -48,12 +49,14 @@ def __init__(
             config: LLM configuration
             verbose: Enable verbose output
             generate_html: Whether to generate HTML viewer
+            commit_id: Git commit SHA for incremental update tracking
         """
         self.repo_path = repo_path
         self.output_dir = output_dir
         self.config = config
         self.verbose = verbose
         self.generate_html = generate_html
+        self.commit_id = commit_id
         self.progress_tracker = ProgressTracker(total_stages=5, verbose=verbose)
         self.job = DocumentationJob()
 
@@ -178,7 +181,7 @@ async def _run_backend_generation(self, backend_config: BackendConfig):
             self.progress_tracker.update_stage(0.2, "Initializing dependency analyzer...")
 
         # Create documentation generator
-        doc_generator = DocumentationGenerator(backend_config)
+        doc_generator = DocumentationGenerator(backend_config, commit_id=self.commit_id)
 
         if self.verbose:
             self.progress_tracker.update_stage(0.5, "Parsing source files...")

codewiki/cli/commands/generate.py

@@ -525,6 +525,8 @@ def generate_command(
             agent_instructions_dict = config.agent_instructions.to_dict()
 
         # Create generator
+        # Get commit_id early so it can be stored in metadata.json for --update support
+        commit_id = get_git_commit_hash(repo_path)
         generator = CLIDocumentationGenerator(
             repo_path=repo_path,
             output_dir=output_dir,
@@ -545,7 +547,8 @@ def generate_command(
                 'max_depth': max_depth if max_depth is not None else config.max_depth,
             },
             verbose=verbose,
-            generate_html=github_pages
+            generate_html=github_pages,
+            commit_id=commit_id,
         )
 
         # Run generation
@@ -556,7 +559,6 @@ def generate_command(
 
         # Get repository info
         repo_url = None
-        commit_hash = get_git_commit_hash(repo_path)
         current_branch = get_git_branch(repo_path)
 
         if is_git_repository(repo_path):