mcp-vector-search 1.0.3__py3-none-any.whl → 1.1.22__py3-none-any.whl

mcp_vector_search/cli/commands/visualize.py.original

@@ -1,2536 +0,0 @@
-"""Visualization commands for MCP Vector Search."""
-
-import asyncio
-import json
-import shutil
-from pathlib import Path
-
-import typer
-from loguru import logger
-from rich.console import Console
-from rich.panel import Panel
-
-from ...core.database import ChromaVectorDatabase
-from ...core.embeddings import create_embedding_function
-from ...core.project import ProjectManager
-
-app = typer.Typer(
-    help="Visualize code chunk relationships",
-    no_args_is_help=True,
-)
-console = Console()
-
-
-@app.command()
-def export(
-    output: Path = typer.Option(
-        Path("chunk-graph.json"),
-        "--output",
-        "-o",
-        help="Output file for chunk relationship data",
-    ),
-    file_path: str | None = typer.Option(
-        None,
-        "--file",
-        "-f",
-        help="Export only chunks from specific file (supports wildcards)",
-    ),
-    code_only: bool = typer.Option(
-        False,
-        "--code-only",
-        help="Exclude documentation chunks (text, comment, docstring)",
-    ),
-) -> None:
-    """Export chunk relationships as JSON for D3.js visualization.
-
-    Examples:
-        # Export all chunks
-        mcp-vector-search visualize export
-
-        # Export from specific file
-        mcp-vector-search visualize export --file src/main.py
-
-        # Custom output location
-        mcp-vector-search visualize export -o graph.json
-
-        # Export only code chunks (exclude documentation)
-        mcp-vector-search visualize export --code-only
-    """
-    asyncio.run(_export_chunks(output, file_path, code_only))
-
-
-async def _export_chunks(
-    output: Path, file_filter: str | None, code_only: bool = False
-) -> None:
-    """Export chunk relationship data.
-
-    Args:
-        output: Path to output JSON file
-        file_filter: Optional file pattern to filter chunks
-        code_only: If True, exclude documentation chunks (text, comment, docstring)
-    """
-    try:
-        # Load project
-        project_manager = ProjectManager(Path.cwd())
-
-        if not project_manager.is_initialized():
-            console.print(
-                "[red]Project not initialized. Run 'mcp-vector-search init' first.[/red]"
-            )
-            raise typer.Exit(1)
-
-        config = project_manager.load_config()
-
-        # Get database
-        embedding_function, _ = create_embedding_function(config.embedding_model)
-        database = ChromaVectorDatabase(
-            persist_directory=config.index_path,
-            embedding_function=embedding_function,
-        )
-        await database.initialize()
-
-        # Get all chunks with metadata
-        console.print("[cyan]Fetching chunks from database...[/cyan]")
-        chunks = await database.get_all_chunks()
-
-        # Store database reference for semantic search
-        # We'll pass it in metadata for the visualization
-        graph_database = database
-
-        if len(chunks) == 0:
-            console.print(
-                "[yellow]No chunks found in index. Run 'mcp-vector-search index' first.[/yellow]"
-            )
-            raise typer.Exit(1)
-
-        console.print(f"[green]✓[/green] Retrieved {len(chunks)} chunks")
-
-        # Apply file filter if specified
-        if file_filter:
-            from fnmatch import fnmatch
-
-            chunks = [c for c in chunks if fnmatch(str(c.file_path), file_filter)]
-            console.print(
-                f"[cyan]Filtered to {len(chunks)} chunks matching '{file_filter}'[/cyan]"
-            )
-
-        # Apply code-only filter if requested
-        if code_only:
-            original_count = len(chunks)
-            chunks = [
-                c
-                for c in chunks
-                if c.chunk_type not in ["text", "comment", "docstring"]
-            ]
-            filtered_count = len(chunks)
-            console.print(
-                f"[dim]Filtered out {original_count - filtered_count} documentation chunks "
-                f"({original_count} → {filtered_count} chunks)[/dim]"
-            )
-
-        # Collect subprojects for monorepo support
-        subprojects = {}
-        for chunk in chunks:
-            if chunk.subproject_name and chunk.subproject_name not in subprojects:
-                subprojects[chunk.subproject_name] = {
-                    "name": chunk.subproject_name,
-                    "path": chunk.subproject_path,
-                    "color": _get_subproject_color(
-                        chunk.subproject_name, len(subprojects)
-                    ),
-                }
-
-        # Build graph data structure
-        nodes = []
-        links = []
-        chunk_id_map = {}  # Map chunk IDs to array indices
-        file_nodes = {}  # Track file nodes by path
-        dir_nodes = {}  # Track directory nodes by path
-
-        # Add subproject root nodes for monorepos
-        if subprojects:
-            console.print(
-                f"[cyan]Detected monorepo with {len(subprojects)} subprojects[/cyan]"
-            )
-            for sp_name, sp_data in subprojects.items():
-                node = {
-                    "id": f"subproject_{sp_name}",
-                    "name": sp_name,
-                    "type": "subproject",
-                    "file_path": sp_data["path"] or "",
-                    "start_line": 0,
-                    "end_line": 0,
-                    "complexity": 0,
-                    "color": sp_data["color"],
-                    "depth": 0,
-                }
-                nodes.append(node)
-
-        # Load directory index for enhanced directory metadata
-        console.print("[cyan]Loading directory index...[/cyan]")
-        from ...core.directory_index import DirectoryIndex
-
-        dir_index_path = (
-            project_manager.project_root / ".mcp-vector-search" / "directory_index.json"
-        )
-        dir_index = DirectoryIndex(dir_index_path)
-        dir_index.load()
-
-        # Create directory nodes from directory index
-        console.print(
-            f"[green]✓[/green] Loaded {len(dir_index.directories)} directories"
-        )
-        for dir_path_str, directory in dir_index.directories.items():
-            dir_id = f"dir_{hash(dir_path_str) & 0xFFFFFFFF:08x}"
-            dir_nodes[dir_path_str] = {
-                "id": dir_id,
-                "name": directory.name,
-                "type": "directory",
-                "file_path": dir_path_str,
-                "start_line": 0,
-                "end_line": 0,
-                "complexity": 0,
-                "depth": directory.depth,
-                "dir_path": dir_path_str,
-                "file_count": directory.file_count,
-                "subdirectory_count": directory.subdirectory_count,
-                "total_chunks": directory.total_chunks,
-                "languages": directory.languages or {},
-                "is_package": directory.is_package,
-                "last_modified": directory.last_modified,
-            }
-
-        # Create file nodes from chunks
-        for chunk in chunks:
-            file_path_str = str(chunk.file_path)
-            file_path = Path(file_path_str)
-
-            # Create file node with parent directory reference
-            if file_path_str not in file_nodes:
-                file_id = f"file_{hash(file_path_str) & 0xFFFFFFFF:08x}"
-
-                # Convert absolute path to relative path for parent directory lookup
-                try:
-                    relative_file_path = file_path.relative_to(
-                        project_manager.project_root
-                    )
-                    parent_dir = relative_file_path.parent
-                    # Use relative path for parent directory (matches directory_index)
-                    parent_dir_str = (
-                        str(parent_dir) if parent_dir != Path(".") else None
-                    )
-                except ValueError:
-                    # File is outside project root
-                    parent_dir_str = None
-
-                # Look up parent directory ID from dir_nodes (must match exactly)
-                parent_dir_id = None
-                if parent_dir_str and parent_dir_str in dir_nodes:
-                    parent_dir_id = dir_nodes[parent_dir_str]["id"]
-
-                file_nodes[file_path_str] = {
-                    "id": file_id,
-                    "name": file_path.name,
-                    "type": "file",
-                    "file_path": file_path_str,
-                    "start_line": 0,
-                    "end_line": 0,
-                    "complexity": 0,
-                    "depth": len(file_path.parts) - 1,
-                    "parent_dir_id": parent_dir_id,
-                    "parent_dir_path": parent_dir_str,
-                }
-
-        # Add directory nodes to graph
-        for dir_node in dir_nodes.values():
-            nodes.append(dir_node)
-
-        # Add file nodes to graph
-        for file_node in file_nodes.values():
-            nodes.append(file_node)
-
-        # Compute semantic relationships for code chunks
-        console.print("[cyan]Computing semantic relationships...[/cyan]")
-        code_chunks = [
-            c for c in chunks if c.chunk_type in ["function", "method", "class"]
-        ]
-        semantic_links = []
-
-        # Pre-compute top 5 semantic relationships for each code chunk
-        for i, chunk in enumerate(code_chunks):
-            if i % 20 == 0:  # Progress indicator every 20 chunks
-                console.print(f"[dim]Processed {i}/{len(code_chunks)} chunks[/dim]")
-
-            try:
-                # Search for similar chunks using the chunk's content
-                similar_results = await graph_database.search(
-                    query=chunk.content[:500],  # Use first 500 chars for query
-                    limit=6,  # Get 6 (exclude self = 5)
-                    similarity_threshold=0.3,  # Lower threshold to catch more relationships
-                )
-
-                # Filter out self and create semantic links
-                for result in similar_results:
-                    # Construct target chunk_id from file_path and line numbers
-                    # This matches the chunk ID construction in the database
-                    target_chunk = next(
-                        (
-                            c
-                            for c in chunks
-                            if str(c.file_path) == str(result.file_path)
-                            and c.start_line == result.start_line
-                            and c.end_line == result.end_line
-                        ),
-                        None,
-                    )
-
-                    if not target_chunk:
-                        continue
-
-                    target_chunk_id = target_chunk.chunk_id or target_chunk.id
-
-                    # Skip self-references
-                    if target_chunk_id == (chunk.chunk_id or chunk.id):
-                        continue
-
-                    # Add semantic link with similarity score (use similarity_score from SearchResult)
-                    if result.similarity_score >= 0.2:
-                        semantic_links.append(
-                            {
-                                "source": chunk.chunk_id or chunk.id,
-                                "target": target_chunk_id,
-                                "type": "semantic",
-                                "similarity": result.similarity_score,
-                            }
-                        )
-
-                        # Only keep top 5
-                        if (
-                            len(
-                                [
-                                    link
-                                    for link in semantic_links
-                                    if link["source"] == (chunk.chunk_id or chunk.id)
-                                ]
-                            )
-                            >= 5
-                        ):
-                            break
-
-            except Exception as e:
-                logger.debug(
-                    f"Failed to compute semantic relationships for {chunk.chunk_id}: {e}"
-                )
-                continue
-
-        console.print(
-            f"[green]✓[/green] Computed {len(semantic_links)} semantic relationships"
-        )
-
-        # Compute external caller relationships
-        console.print("[cyan]Computing external caller relationships...[/cyan]")
-        caller_map = {}  # Map chunk_id -> list of caller info
-
-        for chunk in code_chunks:
-            chunk_id = chunk.chunk_id or chunk.id
-            file_path = str(chunk.file_path)
-            function_name = chunk.function_name or chunk.class_name
-
-            if not function_name:
-                continue
-
-            # Search for other chunks that reference this function/class name
-            for other_chunk in chunks:
-                other_file_path = str(other_chunk.file_path)
-
-                # Only track EXTERNAL callers (different file)
-                if other_file_path == file_path:
-                    continue
-
-                # Check if the other chunk's content mentions this function/class
-                if function_name in other_chunk.content:
-                    other_chunk_id = other_chunk.chunk_id or other_chunk.id
-                    other_name = (
-                        other_chunk.function_name
-                        or other_chunk.class_name
-                        or f"L{other_chunk.start_line}"
-                    )
-
-                    if chunk_id not in caller_map:
-                        caller_map[chunk_id] = []
-
-                    # Store caller information
-                    caller_map[chunk_id].append(
-                        {
-                            "file": other_file_path,
-                            "chunk_id": other_chunk_id,
-                            "name": other_name,
-                            "type": other_chunk.chunk_type,
-                        }
-                    )
-
-        # Count total caller relationships
-        total_callers = sum(len(callers) for callers in caller_map.values())
-        console.print(
-            f"[green]✓[/green] Found {total_callers} external caller relationships"
-        )
-
-        # Detect circular dependencies in caller relationships
-        console.print("[cyan]Detecting circular dependencies...[/cyan]")
-
-        def detect_cycles(nodes_list, links_list):
-            """Detect cycles in the call graph using DFS.
-
-            Returns:
-                List of cycles found, where each cycle is a list of node IDs in the cycle path.
-            """
-            cycles_found = []
-            visited = set()
-
-            def dfs(node_id, path, path_set):
-                """DFS traversal to detect cycles.
-
-                Args:
-                    node_id: Current node ID being visited
-                    path: List of node IDs in current path (for cycle reconstruction)
-                    path_set: Set of node IDs in current path (for O(1) cycle detection)
-
-                Returns:
-                    True if cycle detected in this path
-                """
-                if node_id in path_set:
-                    # Found a cycle! Record the cycle path
-                    cycle_start = path.index(node_id)
-                    cycle_nodes = path[cycle_start:]
-                    cycles_found.append(cycle_nodes)
-                    return True
-
-                if node_id in visited:
-                    return False
-
-                path.append(node_id)
-                path_set.add(node_id)
-                visited.add(node_id)
-
-                # Follow caller links (external callers create directed edges)
-                if node_id in caller_map:
-                    for caller_info in caller_map[node_id]:
-                        caller_id = caller_info["chunk_id"]
-                        dfs(caller_id, path, path_set)
-
-                path.pop()
-                path_set.remove(node_id)
-                return False
-
-            # Run DFS from each unvisited node
-            for node in nodes_list:
-                if node.chunk_id or node.id not in visited:
-                    chunk_id = node.chunk_id or node.id
-                    dfs(chunk_id, [], set())
-
-            return cycles_found
-
-        # Detect cycles
-        cycles = detect_cycles(chunks, [])
-
-        # Mark cycle links
-        cycle_links = []
-        if cycles:
-            console.print(
-                f"[yellow]⚠ Found {len(cycles)} circular dependencies[/yellow]"
-            )
-
-            # For each cycle, create links marking the cycle
-            for cycle in cycles:
-                # Create links for the cycle path: A → B → C → A
-                for i in range(len(cycle)):
-                    source = cycle[i]
-                    target = cycle[(i + 1) % len(cycle)]  # Wrap around to form cycle
-                    cycle_links.append(
-                        {
-                            "source": source,
-                            "target": target,
-                            "type": "caller",
-                            "is_cycle": True,
-                        }
-                    )
-        else:
-            console.print("[green]✓[/green] No circular dependencies detected")
-
-        # Add chunk nodes
-        for chunk in chunks:
-            chunk_id = chunk.chunk_id or chunk.id
-            node = {
-                "id": chunk_id,
-                "name": chunk.function_name
-                or chunk.class_name
-                or f"L{chunk.start_line}",
-                "type": chunk.chunk_type,
-                "file_path": str(chunk.file_path),
-                "start_line": chunk.start_line,
-                "end_line": chunk.end_line,
-                "complexity": chunk.complexity_score,
-                "parent_id": chunk.parent_chunk_id,
-                "depth": chunk.chunk_depth,
-                "content": chunk.content,  # Add content for code viewer
-                "docstring": chunk.docstring,
-                "language": chunk.language,
-            }
-
-            # Add caller information if available
-            if chunk_id in caller_map:
-                node["callers"] = caller_map[chunk_id]
-
-            # Add subproject info for monorepos
-            if chunk.subproject_name:
-                node["subproject"] = chunk.subproject_name
-                node["color"] = subprojects[chunk.subproject_name]["color"]
-
-            nodes.append(node)
-            chunk_id_map[node["id"]] = len(nodes) - 1
-
-        # Link directories to their parent directories (hierarchical structure)
-        for dir_path_str, dir_info in dir_index.directories.items():
-            if dir_info.parent_path:
-                parent_path_str = str(dir_info.parent_path)
-                if parent_path_str in dir_nodes:
-                    parent_dir_id = f"dir_{hash(parent_path_str) & 0xFFFFFFFF:08x}"
-                    child_dir_id = f"dir_{hash(dir_path_str) & 0xFFFFFFFF:08x}"
-                    links.append(
-                        {
-                            "source": parent_dir_id,
-                            "target": child_dir_id,
-                            "type": "dir_hierarchy",
-                        }
-                    )
-
-        # Link directories to subprojects in monorepos (simple flat structure)
-        if subprojects:
-            for dir_path_str, dir_node in dir_nodes.items():
-                for sp_name, sp_data in subprojects.items():
-                    if dir_path_str.startswith(sp_data.get("path", "")):
-                        links.append(
-                            {
-                                "source": f"subproject_{sp_name}",
-                                "target": dir_node["id"],
-                                "type": "dir_containment",
-                            }
-                        )
-                        break
-
-        # Link files to their parent directories
-        for _file_path_str, file_node in file_nodes.items():
-            if file_node.get("parent_dir_id"):
-                links.append(
-                    {
-                        "source": file_node["parent_dir_id"],
-                        "target": file_node["id"],
-                        "type": "dir_containment",
-                    }
-                )
-
-        # Build hierarchical links from parent-child relationships
-        for chunk in chunks:
-            chunk_id = chunk.chunk_id or chunk.id
-            file_path = str(chunk.file_path)
-
-            # Link chunk to its file node if it has no parent (top-level chunks)
-            if not chunk.parent_chunk_id and file_path in file_nodes:
-                links.append(
-                    {
-                        "source": file_nodes[file_path]["id"],
-                        "target": chunk_id,
-                        "type": "file_containment",
-                    }
-                )
-
-            # Link to subproject root if in monorepo
-            if chunk.subproject_name and not chunk.parent_chunk_id:
-                links.append(
-                    {
-                        "source": f"subproject_{chunk.subproject_name}",
-                        "target": chunk_id,
-                    }
-                )
-
-            # Link to parent chunk
-            if chunk.parent_chunk_id and chunk.parent_chunk_id in chunk_id_map:
-                links.append(
-                    {
-                        "source": chunk.parent_chunk_id,
-                        "target": chunk_id,
-                    }
-                )
-
-        # Add semantic relationship links
-        links.extend(semantic_links)
-
-        # Add cycle links
-        links.extend(cycle_links)
-
-        # Parse inter-project dependencies for monorepos
-        if subprojects:
-            console.print("[cyan]Parsing inter-project dependencies...[/cyan]")
-            dep_links = _parse_project_dependencies(
-                project_manager.project_root, subprojects
-            )
-            links.extend(dep_links)
-            if dep_links:
-                console.print(
-                    f"[green]✓[/green] Found {len(dep_links)} inter-project dependencies"
-                )
-
-        # Get stats
-        stats = await database.get_stats()
-
-        # Build final graph data
-        graph_data = {
-            "nodes": nodes,
-            "links": links,
-            "metadata": {
-                "total_chunks": len(chunks),
-                "total_files": stats.total_files,
-                "languages": stats.languages,
-                "is_monorepo": len(subprojects) > 0,
-                "subprojects": list(subprojects.keys()) if subprojects else [],
-            },
-        }
-
-        # Write to file
-        output.parent.mkdir(parents=True, exist_ok=True)
-        with open(output, "w") as f:
-            json.dump(graph_data, f, indent=2)
-
-        await database.close()
-
-        console.print()
-        cycle_warning = f"[yellow]Cycles: {len(cycles)} ⚠️[/yellow]\n" if cycles else ""
-        console.print(
-            Panel.fit(
-                f"[green]✓[/green] Exported graph data to [cyan]{output}[/cyan]\n\n"
-                f"Nodes: {len(graph_data['nodes'])}\n"
-                f"Links: {len(graph_data['links'])}\n"
-                f"{cycle_warning}"
-                f"{'Subprojects: ' + str(len(subprojects)) if subprojects else ''}\n\n"
-                f"[dim]Next: Run 'mcp-vector-search visualize serve' to view[/dim]",
-                title="Export Complete",
-                border_style="green",
-            )
-        )
-
-    except Exception as e:
-        logger.error(f"Export failed: {e}")
-        console.print(f"[red]✗ Export failed: {e}[/red]")
-        raise typer.Exit(1)
-
-
-def _get_subproject_color(subproject_name: str, index: int) -> str:
-    """Get a consistent color for a subproject."""
-    # Color palette for subprojects (GitHub-style colors)
-    colors = [
-        "#238636",  # Green
-        "#1f6feb",  # Blue
-        "#d29922",  # Yellow
-        "#8957e5",  # Purple
-        "#da3633",  # Red
-        "#bf8700",  # Orange
-        "#1a7f37",  # Dark green
-        "#0969da",  # Dark blue
-    ]
-    return colors[index % len(colors)]
-
-
-def _parse_project_dependencies(project_root: Path, subprojects: dict) -> list[dict]:
-    """Parse package.json files to find inter-project dependencies.
-
-    Args:
-        project_root: Root directory of the monorepo
-        subprojects: Dictionary of subproject information
-
-    Returns:
-        List of dependency links between subprojects
-    """
-    dependency_links = []
-
-    for sp_name, sp_data in subprojects.items():
-        package_json = project_root / sp_data["path"] / "package.json"
-
-        if not package_json.exists():
-            continue
-
-        try:
-            with open(package_json) as f:
-                package_data = json.load(f)
-
-            # Check all dependency types
-            all_deps = {}
-            for dep_type in ["dependencies", "devDependencies", "peerDependencies"]:
-                if dep_type in package_data:
-                    all_deps.update(package_data[dep_type])
-
-            # Find dependencies on other subprojects
-            for dep_name in all_deps.keys():
-                # Check if this dependency is another subproject
-                for other_sp_name in subprojects.keys():
-                    if other_sp_name != sp_name and dep_name == other_sp_name:
-                        # Found inter-project dependency
-                        dependency_links.append(
-                            {
-                                "source": f"subproject_{sp_name}",
-                                "target": f"subproject_{other_sp_name}",
-                                "type": "dependency",
-                            }
-                        )
-
-        except Exception as e:
-            logger.debug(f"Failed to parse {package_json}: {e}")
-            continue
-
-    return dependency_links
-
-
-@app.command()
-def serve(
-    port: int = typer.Option(
-        8080, "--port", "-p", help="Port for visualization server"
-    ),
-    graph_file: Path = typer.Option(
-        Path("chunk-graph.json"),
-        "--graph",
-        "-g",
-        help="Graph JSON file to visualize",
-    ),
-    code_only: bool = typer.Option(
-        False,
-        "--code-only",
-        help="Exclude documentation chunks (text, comment, docstring)",
-    ),
-) -> None:
-    """Start local HTTP server for D3.js visualization.
-
-    Examples:
-        # Start server on default port 8080
-        mcp-vector-search visualize serve
-
-        # Custom port
-        mcp-vector-search visualize serve --port 3000
-
-        # Custom graph file
-        mcp-vector-search visualize serve --graph my-graph.json
-
-        # Serve with code-only filter
-        mcp-vector-search visualize serve --code-only
-    """
-    import http.server
-    import os
-    import socket
-    import socketserver
-    import webbrowser
-
-    # Find free port in range 8080-8099
-    def find_free_port(start_port: int = 8080, end_port: int = 8099) -> int:
-        """Find a free port in the given range."""
-        for test_port in range(start_port, end_port + 1):
-            try:
-                with socket.socket(socket.AF_INET, socket.SOCK_STREAM) as s:
-                    s.bind(("", test_port))
-                    return test_port
-            except OSError:
-                continue
-        raise OSError(f"No free ports available in range {start_port}-{end_port}")
-
-    # Use specified port or find free one
-    if port == 8080:  # Default port, try to find free one
-        try:
-            port = find_free_port(8080, 8099)
-        except OSError as e:
-            console.print(f"[red]✗ {e}[/red]")
-            raise typer.Exit(1)
-
-    # Get visualization directory - use project-local storage
-    project_manager = ProjectManager(Path.cwd())
-    if not project_manager.is_initialized():
-        console.print(
-            "[red]Project not initialized. Run 'mcp-vector-search init' first.[/red]"
-        )
-        raise typer.Exit(1)
-
-    viz_dir = project_manager.project_root / ".mcp-vector-search" / "visualization"
-
-    if not viz_dir.exists():
-        console.print(
-            f"[yellow]Visualization directory not found. Creating at {viz_dir}...[/yellow]"
-        )
-        viz_dir.mkdir(parents=True, exist_ok=True)
-
-    # Always ensure index.html exists (regenerate if missing)
-    html_file = viz_dir / "index.html"
-    if not html_file.exists():
-        console.print("[yellow]Creating visualization HTML file...[/yellow]")
-        _create_visualization_html(html_file)
-
-    # Check if we need to regenerate the graph file
-    needs_regeneration = not graph_file.exists() or code_only
-
-    if graph_file.exists() and not needs_regeneration:
-        # Use existing unfiltered file
-        dest = viz_dir / "chunk-graph.json"
-        shutil.copy(graph_file, dest)
-        console.print(f"[green]✓[/green] Copied graph data to {dest}")
-    else:
-        # Generate new file (with filter if requested)
-        if graph_file.exists() and code_only:
-            console.print(
-                "[yellow]Regenerating filtered graph data (--code-only)...[/yellow]"
-            )
-        elif not graph_file.exists():
-            console.print(
-                f"[yellow]Graph file {graph_file} not found. Generating it now...[/yellow]"
-            )
-
-        asyncio.run(_export_chunks(graph_file, None, code_only))
-        console.print()
-
-        # Copy the newly generated graph to visualization directory
-        if graph_file.exists():
-            dest = viz_dir / "chunk-graph.json"
-            shutil.copy(graph_file, dest)
-            console.print(f"[green]✓[/green] Copied graph data to {dest}")
-
-    # Change to visualization directory
-    os.chdir(viz_dir)
-
-    # Start server
-    handler = http.server.SimpleHTTPRequestHandler
-    try:
-        with socketserver.TCPServer(("", port), handler) as httpd:
-            url = f"http://localhost:{port}"
-            console.print()
-            console.print(
-                Panel.fit(
-                    f"[green]✓[/green] Visualization server running\n\n"
-                    f"URL: [cyan]{url}[/cyan]\n"
-                    f"Directory: [dim]{viz_dir}[/dim]\n\n"
-                    f"[dim]Press Ctrl+C to stop[/dim]",
-                    title="Server Started",
-                    border_style="green",
-                )
-            )
-
-            # Open browser
-            webbrowser.open(url)
-
-            try:
-                httpd.serve_forever()
-            except KeyboardInterrupt:
-                console.print("\n[yellow]Stopping server...[/yellow]")
-
-    except OSError as e:
-        if "Address already in use" in str(e):
-            console.print(
-                f"[red]✗ Port {port} is already in use. Try a different port with --port[/red]"
-            )
-        else:
-            console.print(f"[red]✗ Server error: {e}[/red]")
-        raise typer.Exit(1)
-
-
-def _create_visualization_html(html_file: Path) -> None:
-    """Create the D3.js visualization HTML file."""
-    html_content = """<!DOCTYPE html>
-<html>
-<head>
-    <meta charset="utf-8">
-    <title>Code Chunk Relationship Graph</title>
-    <script src="https://d3js.org/d3.v7.min.js"></script>
-    <style>
-        body {
-            margin: 0;
-            font-family: -apple-system, BlinkMacSystemFont, "Segoe UI", Roboto, sans-serif;
-            background: #0d1117;
-            color: #c9d1d9;
-            overflow: hidden;
-        }
-
-        #controls {
-            position: absolute;
-            top: 20px;
-            left: 20px;
-            background: rgba(13, 17, 23, 0.95);
-            border: 1px solid #30363d;
-            border-radius: 6px;
-            padding: 16px;
-            min-width: 250px;
-            max-height: 80vh;
-            overflow-y: auto;
-            box-shadow: 0 8px 24px rgba(0, 0, 0, 0.4);
-        }
-
-        h1 { margin: 0 0 16px 0; font-size: 18px; }
-        h3 { margin: 16px 0 8px 0; font-size: 14px; color: #8b949e; }
-
-        .control-group {
-            margin-bottom: 12px;
-        }
-
-        label {
-            display: block;
-            margin-bottom: 4px;
-            font-size: 12px;
-            color: #8b949e;
-        }
-
-        input[type="file"] {
-            width: 100%;
-            padding: 6px;
-            background: #161b22;
-            border: 1px solid #30363d;
-            border-radius: 6px;
-            color: #c9d1d9;
-            font-size: 12px;
-        }
-
-        .legend {
-            font-size: 12px;
-        }
-
-        .legend-item {
-            margin: 4px 0;
-            display: flex;
-            align-items: center;
-        }
-
-        .legend-color {
-            width: 12px;
-            height: 12px;
-            border-radius: 50%;
-            margin-right: 8px;
-        }
-
-        #graph {
-            width: 100vw;
-            height: 100vh;
-        }
-
-        .node circle {
-            cursor: pointer;
-            stroke: #c9d1d9;
-            stroke-width: 2px;
-            pointer-events: all;
-        }
-
-        .node.module circle { fill: #238636; }
-        .node.class circle { fill: #1f6feb; }
-        .node.function circle { fill: #d29922; }
-        .node.method circle { fill: #8957e5; }
-        .node.code circle { fill: #6e7681; }
-        .node.file circle {
-            fill: none;
-            stroke: #58a6ff;
-            stroke-width: 2px;
-            stroke-dasharray: 5,3;
-            opacity: 0.6;
-        }
-        .node.directory circle {
-            fill: none;
-            stroke: #79c0ff;
-            stroke-width: 2px;
-            stroke-dasharray: 3,3;
-            opacity: 0.5;
-        }
-        .node.subproject circle { fill: #da3633; stroke-width: 3px; }
-
-        /* Non-code document nodes - squares */
-        .node.docstring rect { fill: #8b949e; }
-        .node.comment rect { fill: #6e7681; }
-        .node rect {
-            cursor: pointer;
-            stroke: #c9d1d9;
-            stroke-width: 2px;
-            pointer-events: all;
-        }
-
-        /* File type icon styling */
-        .node path.file-icon {
-            fill: currentColor;
-            stroke: none;
-            pointer-events: all;
-            cursor: pointer;
-        }
-
-        .node text {
-            font-size: 14px;
-            fill: #c9d1d9;
-            text-anchor: middle;
-            pointer-events: none;
-            user-select: none;
-        }
-
-        .link {
-            stroke: #30363d;
-            stroke-opacity: 0.6;
-            stroke-width: 1.5px;
-        }
-
-        .link.dependency {
-            stroke: #d29922;
-            stroke-opacity: 0.8;
-            stroke-width: 2px;
-            stroke-dasharray: 5,5;
-        }
-
-        /* Semantic relationship links - colored by similarity */
-        .link.semantic {
-            stroke-opacity: 0.7;
-            stroke-dasharray: 4,4;
-        }
-
-        .link.semantic.sim-high { stroke: #00ff00; stroke-width: 4px; }
-        .link.semantic.sim-medium-high { stroke: #88ff00; stroke-width: 3px; }
-        .link.semantic.sim-medium { stroke: #ffff00; stroke-width: 2.5px; }
-        .link.semantic.sim-low { stroke: #ffaa00; stroke-width: 2px; }
-        .link.semantic.sim-very-low { stroke: #ff0000; stroke-width: 1.5px; }
-
-        /* Circular dependency links - highest visual priority */
-        .link.cycle {
-            stroke: #ff4444 !important;
-            stroke-width: 3px !important;
-            stroke-dasharray: 8, 4;
-            stroke-opacity: 0.8;
-            animation: pulse-cycle 2s infinite;
-        }
-
-        @keyframes pulse-cycle {
-            0%, 100% { stroke-opacity: 0.8; }
-            50% { stroke-opacity: 1.0; }
-        }
-
-        .tooltip {
-            position: absolute;
-            padding: 12px;
-            background: rgba(13, 17, 23, 0.95);
-            border: 1px solid #30363d;
-            border-radius: 6px;
-            pointer-events: none;
-            display: none;
-            font-size: 12px;
-            max-width: 300px;
-            box-shadow: 0 8px 24px rgba(0, 0, 0, 0.4);
-        }
-
-        .stats {
-            margin-top: 16px;
-            padding-top: 16px;
-            border-top: 1px solid #30363d;
-            font-size: 12px;
-            color: #8b949e;
-        }
-
-        #content-pane {
-            position: fixed;
-            top: 0;
-            right: 0;
-            width: 600px;
-            height: 100vh;
-            background: rgba(13, 17, 23, 0.98);
-            border-left: 1px solid #30363d;
-            overflow-y: auto;
-            box-shadow: -4px 0 24px rgba(0, 0, 0, 0.5);
-            transform: translateX(100%);
-            transition: transform 0.3s ease-in-out;
-            z-index: 1000;
-        }
-
-        #content-pane.visible {
-            transform: translateX(0);
-        }
-
-        #content-pane .pane-header {
-            position: sticky;
-            top: 0;
-            background: rgba(13, 17, 23, 0.98);
-            padding: 20px;
-            border-bottom: 1px solid #30363d;
-            z-index: 1;
-        }
-
-        #content-pane .pane-title {
-            font-size: 16px;
-            font-weight: bold;
-            color: #58a6ff;
-            margin-bottom: 8px;
-            padding-right: 30px;
-        }
-
-        #content-pane .pane-meta {
-            font-size: 12px;
-            color: #8b949e;
-        }
-
-        #content-pane .pane-footer {
-            position: sticky;
-            bottom: 0;
-            background: rgba(13, 17, 23, 0.98);
-            padding: 16px 20px;
-            border-top: 1px solid #30363d;
-            font-size: 11px;
-            color: #8b949e;
-            z-index: 1;
-        }
-
-        #content-pane .pane-footer .footer-item {
-            display: block;
-            margin-bottom: 8px;
-        }
-
-        #content-pane .pane-footer .footer-label {
-            color: #c9d1d9;
-            font-weight: 600;
-            margin-right: 4px;
-        }
-
-        #content-pane .pane-footer .footer-value {
-            color: #8b949e;
-        }
-
-        #content-pane .collapse-btn {
-            position: absolute;
-            top: 20px;
-            right: 20px;
-            cursor: pointer;
-            color: #8b949e;
-            font-size: 24px;
-            line-height: 1;
-            background: none;
-            border: none;
-            padding: 0;
-            transition: color 0.2s;
-        }
-
-        #content-pane .collapse-btn:hover {
-            color: #c9d1d9;
-        }
-
-        #content-pane .pane-content {
-            padding: 20px;
-        }
-
-        #content-pane pre {
-            margin: 0;
-            padding: 16px;
-            background: #0d1117;
-            border: 1px solid #30363d;
-            border-radius: 6px;
-            overflow-x: auto;
-            font-size: 12px;
-            line-height: 1.6;
-        }
-
-        #content-pane code {
-            color: #c9d1d9;
-            font-family: 'Monaco', 'Menlo', 'Ubuntu Mono', monospace;
-        }
-
-        #content-pane .directory-list {
-            list-style: none;
-            padding: 0;
-            margin: 0;
-        }
-
-        #content-pane .directory-list li {
-            padding: 8px 12px;
-            margin: 4px 0;
-            background: #161b22;
-            border: 1px solid #30363d;
-            border-radius: 4px;
-            font-size: 12px;
-            display: flex;
-            align-items: center;
-            cursor: pointer;
-            transition: background-color 0.2s;
-        }
-
-        #content-pane .directory-list li:hover {
-            background-color: rgba(255, 255, 255, 0.1);
-        }
-
-        #content-pane .directory-list .item-icon {
-            margin-right: 8px;
-            font-size: 14px;
-        }
-
-        #content-pane .directory-list .item-type {
-            margin-left: auto;
-            padding-left: 12px;
-            font-size: 10px;
-            color: #8b949e;
-        }
-
-        #content-pane .import-details {
-            background: #161b22;
-            border: 1px solid #30363d;
-            border-radius: 6px;
-            padding: 16px;
-        }
-
-        #content-pane .import-details .import-statement {
-            font-family: 'Monaco', 'Menlo', 'Ubuntu Mono', monospace;
-            font-size: 12px;
-            color: #79c0ff;
-            margin-bottom: 12px;
-        }
-
-        #content-pane .import-details .detail-row {
-            font-size: 11px;
-            color: #8b949e;
-            margin: 4px 0;
-        }
-
-        #content-pane .import-details .detail-label {
-            color: #c9d1d9;
-            font-weight: 600;
-        }
-
-        .node.highlighted circle,
-        .node.highlighted rect {
-            stroke: #f0e68c;
-            stroke-width: 3px;
-            filter: drop-shadow(0 0 8px #f0e68c);
-        }
-
-        .caller-link {
-            color: #58a6ff;
-            text-decoration: none;
-            cursor: pointer;
-            transition: color 0.2s;
-        }
-
-        .caller-link:hover {
-            color: #79c0ff;
-            text-decoration: underline;
-        }
-
-        #reset-view-btn {
-            position: fixed;
-            top: 20px;
-            right: 460px;
-            padding: 8px 16px;
-            background: #21262d;
-            border: 1px solid #30363d;
-            border-radius: 6px;
-            color: #c9d1d9;
-            font-size: 14px;
-            cursor: pointer;
-            display: flex;
-            align-items: center;
-            gap: 8px;
-            z-index: 100;
-            transition: all 0.2s;
-        }
-
-        #reset-view-btn:hover {
-            background: #30363d;
-            border-color: #58a6ff;
-            transform: translateY(-1px);
-            box-shadow: 0 4px 8px rgba(0, 0, 0, 0.2);
-        }
-
-        /* Loading spinner animation */
-        @keyframes spin {
-            0% { transform: rotate(0deg); }
-            100% { transform: rotate(360deg); }
-        }
-
-        .spinner {
-            display: inline-block;
-            width: 20px;
-            height: 20px;
-            border: 3px solid #30363d;
-            border-top-color: #58a6ff;
-            border-radius: 50%;
-            animation: spin 0.8s linear infinite;
-            margin-right: 8px;
-            vertical-align: middle;
-        }
-    </style>
-</head>
-<body>
-    <div id="controls">
-        <h1>🔍 Code Graph</h1>
-
-        <div class="control-group" id="loading">
-            <label>⏳ Loading graph data...</label>
-        </div>
-
-        <h3>Legend</h3>
-        <div class="legend">
-            <div class="legend-item">
-                <span class="legend-color" style="background: #da3633;"></span> Subproject
-            </div>
-            <div class="legend-item">
-                📁 Directory
-            </div>
-            <div class="legend-item">
-                📄 File (.py 🐍 .js/.ts 📜 .md 📝 .json/.yaml ⚙️ .sh 💻)
-            </div>
-            <div class="legend-item">
-                <span class="legend-color" style="background: #238636;"></span> Module
-            </div>
-            <div class="legend-item">
-                <span class="legend-color" style="background: #1f6feb;"></span> Class
-            </div>
-            <div class="legend-item">
-                <span class="legend-color" style="background: #d29922;"></span> Function
-            </div>
-            <div class="legend-item">
-                <span class="legend-color" style="background: #8957e5;"></span> Method
-            </div>
-            <div class="legend-item">
-                <span class="legend-color" style="background: #6e7681;"></span> Code
-            </div>
-            <div class="legend-item" style="font-style: italic; color: #79c0ff;">
-                <span class="legend-color" style="background: #6e7681;"></span> Import (L1)
-            </div>
-            <div class="legend-item">
-                <span class="legend-color" style="background: #8b949e; border-radius: 2px;"></span> Docstring ▢
-            </div>
-            <div class="legend-item">
-                <span class="legend-color" style="background: #6e7681; border-radius: 2px;"></span> Comment ▢
-            </div>
-        </div>
-
-        <h3>Relationships</h3>
-        <div class="legend">
-            <div class="legend-item" style="color: #ff4444;">
-                ⚠️ Circular Dependency (red pulsing)
-            </div>
-            <div class="legend-item" style="color: #00ff00;">
-                — Semantic (green-yellow gradient)
-            </div>
-            <div class="legend-item" style="color: #30363d;">
-                — Structural (gray)
-            </div>
-        </div>
-
-        <div id="subprojects-legend" style="display: none;">
-            <h3>Subprojects</h3>
-            <div class="legend" id="subprojects-list"></div>
-        </div>
-
-        <div class="stats" id="stats"></div>
-    </div>
-
-    <svg id="graph"></svg>
-    <div id="tooltip" class="tooltip"></div>
-
-    <button id="reset-view-btn" title="Reset to home view">
-        <span style="font-size: 18px;">🏠</span>
-        <span>Reset View</span>
-    </button>
-
-    <div id="content-pane">
-        <div class="pane-header">
-            <button class="collapse-btn" onclick="closeContentPane()">×</button>
-            <div class="pane-title" id="pane-title"></div>
-            <div class="pane-meta" id="pane-meta"></div>
-        </div>
-        <div class="pane-content" id="pane-content"></div>
-        <div class="pane-footer" id="pane-footer"></div>
-    </div>
-
-    <script>
-        const width = window.innerWidth;
-        const height = window.innerHeight;
-
-        // Create zoom behavior
-        const zoom = d3.zoom().on("zoom", (event) => {
-            g.attr("transform", event.transform);
-        });
-
-        const svg = d3.select("#graph")
-            .attr("width", width)
-            .attr("height", height)
-            .call(zoom);
-
-        const g = svg.append("g");
-        const tooltip = d3.select("#tooltip");
-        let simulation;
-        let allNodes = [];
-        let allLinks = [];
-        let visibleNodes = new Set();
-        let collapsedNodes = new Set();
-        let highlightedNode = null;
-        let rootNodes = [];  // NEW: Store root nodes for reset function
-
-        // Get file extension from path
-        function getFileExtension(filePath) {
-            if (!filePath) return '';
-            const match = filePath.match(/\\.([^.]+)$/);
-            return match ? match[1].toLowerCase() : '';
-        }
-
-        // Get SVG icon path for file type
-        function getFileTypeIcon(node) {
-            if (node.type === 'directory') {
-                // Folder icon
-                return 'M10 4H4c-1.1 0-2 .9-2 2v12c0 1.1.9 2 2 2h16c1.1 0 2-.9 2-2V8c0-1.1-.9-2-2-2h-8l-2-2z';
-            }
-            if (node.type === 'file') {
-                const ext = getFileExtension(node.file_path);
-
-                // Python files
-                if (ext === 'py') {
-                    return 'M12 2C6.48 2 2 6.48 2 12s4.48 10 10 10 10-4.48 10-10S17.52 2 12 2zm0 18c-4.41 0-8-3.59-8-8s3.59-8 8-8 8 3.59 8 8-3.59 8-8 8zm-1-13h2v6h-2zm0 8h2v2h-2z';
-                }
-                // JavaScript/TypeScript
-                if (ext === 'js' || ext === 'jsx' || ext === 'ts' || ext === 'tsx') {
-                    return 'M3 3h18v18H3V3zm16 16V5H5v14h14zM7 7h2v2H7V7zm4 0h2v2h-2V7zm-4 4h2v2H7v-2zm4 0h6v2h-6v-2zm-4 4h10v2H7v-2z';
-                }
-                // Markdown
-                if (ext === 'md' || ext === 'markdown') {
-                    return 'M14 2H6c-1.1 0-2 .9-2 2v16c0 1.1.9 2 2 2h12c1.1 0 2-.9 2-2V8l-6-6zM6 20V4h7v5h5v11H6zm10-10h-3v2h3v2h-3v2h3v2h-7V8h7v2z';
-                }
-                // JSON/YAML/Config files
-                if (ext === 'json' || ext === 'yaml' || ext === 'yml' || ext === 'toml' || ext === 'ini' || ext === 'conf') {
-                    return 'M14 2H6c-1.1 0-2 .9-2 2v16c0 1.1.9 2 2 2h12c1.1 0 2-.9 2-2V8l-6-6zm0 2l4 4h-4V4zM6 20V4h6v6h6v10H6zm4-4h4v2h-4v-2zm0-4h4v2h-4v-2z';
-                }
-                // Shell scripts
-                if (ext === 'sh' || ext === 'bash' || ext === 'zsh') {
-                    return 'M20 4H4c-1.1 0-2 .9-2 2v12c0 1.1.9 2 2 2h16c1.1 0 2-.9 2-2V6c0-1.1-.9-2-2-2zm0 14H4V8h16v10zm-2-8h-2v2h2v-2zm0 4h-2v2h2v-2zM6 10h8v2H6v-2z';
-                }
-                // Generic code file
-                return 'M14 2H6c-1.1 0-2 .9-2 2v16c0 1.1.9 2 2 2h12c1.1 0 2-.9 2-2V8l-6-6zm0 2l4 4h-4V4zM6 20V4h6v6h6v10H6zm3-4h6v2H9v-2zm0-4h6v2H9v-2z';
-            }
-            return null;
-        }
-
-        // Get color for file type icon
-        function getFileTypeColor(node) {
-            if (node.type === 'directory') return '#79c0ff';
-            if (node.type === 'file') {
-                const ext = getFileExtension(node.file_path);
-                if (ext === 'py') return '#3776ab';  // Python blue
-                if (ext === 'js' || ext === 'jsx') return '#f7df1e';  // JavaScript yellow
-                if (ext === 'ts' || ext === 'tsx') return '#3178c6';  // TypeScript blue
-                if (ext === 'md' || ext === 'markdown') return '#8b949e';  // Gray
-                if (ext === 'json' || ext === 'yaml' || ext === 'yml') return '#90a4ae';  // Config gray
-                if (ext === 'sh' || ext === 'bash' || ext === 'zsh') return '#4eaa25';  // Shell green
-                return '#58a6ff';  // Default file color
-            }
-            return null;
-        }
-
-        function visualizeGraph(data) {
-            g.selectAll("*").remove();
-
-            allNodes = data.nodes;
-            allLinks = data.links;
-
-            // Find root nodes - start with only top-level nodes
-            let rootNodes;
-            if (data.metadata && data.metadata.is_monorepo) {
-                // In monorepos, subproject nodes are roots
-                rootNodes = allNodes.filter(n => n.type === 'subproject');
-            } else {
-                // Regular projects: show root-level directories AND files
-                const dirNodes = allNodes.filter(n => n.type === 'directory');
-                const fileNodes = allNodes.filter(n => n.type === 'file');
-
-                // Find minimum depth for directories and files
-                const minDirDepth = dirNodes.length > 0
-                    ? Math.min(...dirNodes.map(n => n.depth))
-                    : Infinity;
-                const minFileDepth = fileNodes.length > 0
-                    ? Math.min(...fileNodes.map(n => n.depth))
-                    : Infinity;
-
-                // Include both root-level directories and root-level files
-                rootNodes = [
-                    ...dirNodes.filter(n => n.depth === minDirDepth),
-                    ...fileNodes.filter(n => n.depth === minFileDepth)
-                ];
-
-                // Fallback to all files if nothing found
-                if (rootNodes.length === 0) {
-                    rootNodes = fileNodes;
-                }
-            }
-
-            // Start with only root nodes visible, all collapsed
-            rootNodes = rootNodes;  // Store for reset function
-            visibleNodes = new Set(rootNodes.map(n => n.id));
-            collapsedNodes = new Set(rootNodes.map(n => n.id));
-
-            renderGraph();
-        }
-
-        function renderGraph() {
-            const visibleNodesList = allNodes.filter(n => visibleNodes.has(n.id));
-            const visibleLinks = allLinks.filter(l =>
-                visibleNodes.has(l.source.id || l.source) &&
-                visibleNodes.has(l.target.id || l.target)
-            );
-
-            simulation = d3.forceSimulation(visibleNodesList)
-                .force("link", d3.forceLink(visibleLinks).id(d => d.id).distance(100))
-                .force("charge", d3.forceManyBody().strength(d => {
-                    // Check if node has any connections
-                    const hasConnections = allLinks.some(link =>
-                        link.source.id === d.id || link.target.id === d.id
-                    );
-                    // Connected nodes: spread out more (-200)
-                    // Unconnected nodes: cluster together (-50)
-                    return hasConnections ? -200 : -50;
-                }))
-                .force("center", d3.forceCenter(width / 2, height / 2).strength(0.15))
-                .force("collision", d3.forceCollide().radius(35));
-
-            g.selectAll("*").remove();
-
-            const link = g.append("g")
-                .selectAll("line")
-                .data(visibleLinks)
-                .join("line")
-                .attr("class", d => {
-                    // Cycle links have highest priority
-                    if (d.is_cycle) return "link cycle";
-                    if (d.type === "dependency") return "link dependency";
-                    if (d.type === "semantic") {
-                        // Color based on similarity score
-                        const sim = d.similarity || 0;
-                        let simClass = "sim-very-low";
-                        if (sim >= 0.8) simClass = "sim-high";
-                        else if (sim >= 0.6) simClass = "sim-medium-high";
-                        else if (sim >= 0.4) simClass = "sim-medium";
-                        else if (sim >= 0.2) simClass = "sim-low";
-                        return `link semantic ${simClass}`;
-                    }
-                    return "link";
-                })
-                .on("mouseover", showLinkTooltip)
-                .on("mouseout", hideTooltip);
-
-            const node = g.append("g")
-                .selectAll("g")
-                .data(visibleNodesList)
-                .join("g")
-                .attr("class", d => {
-                    let classes = `node ${d.type}`;
-                    if (highlightedNode && d.id === highlightedNode.id) {
-                        classes += ' highlighted';
-                    }
-                    return classes;
-                })
-                .call(drag(simulation))
-                .on("click", handleNodeClick)
-                .on("mouseover", showTooltip)
-                .on("mouseout", hideTooltip);
-
-            // Add shapes based on node type
-            const isDocNode = d => ['docstring', 'comment'].includes(d.type);
-            const isFileOrDir = d => d.type === 'file' || d.type === 'directory';
-
-            // Add circles for regular code nodes (not files/dirs/docs)
-            node.filter(d => !isDocNode(d) && !isFileOrDir(d))
-                .append("circle")
-                .attr("r", d => {
-                    if (d.type === 'subproject') return 24;
-                    return d.complexity ? Math.min(12 + d.complexity * 2, 28) : 15;
-                })
-                .attr("stroke", d => {
-                    // Check if node has incoming caller/imports edges (dead code detection)
-                    const hasIncoming = allLinks.some(l =>
-                        (l.target.id || l.target) === d.id &&
-                        (l.type === 'caller' || l.type === 'imports')
-                    );
-                    if (!hasIncoming && (d.type === 'function' || d.type === 'class' || d.type === 'method')) {
-                        // Check if it's not an entry point (main, test, cli files)
-                        const isEntryPoint = d.file_path && (
-                            d.file_path.includes('main.py') ||
-                            d.file_path.includes('__main__.py') ||
-                            d.file_path.includes('cli.py') ||
-                            d.file_path.includes('test_')
-                        );
-                        if (!isEntryPoint) {
-                            return "#ff6b6b"; // Red border for potentially dead code
-                        }
-                    }
-                    return hasChildren(d) ? "#ffffff" : "none";
-                })
-                .attr("stroke-width", d => {
-                    const hasIncoming = allLinks.some(l =>
-                        (l.target.id || l.target) === d.id &&
-                        (l.type === 'caller' || l.type === 'imports')
-                    );
-                    if (!hasIncoming && (d.type === 'function' || d.type === 'class' || d.type === 'method')) {
-                        const isEntryPoint = d.file_path && (
-                            d.file_path.includes('main.py') ||
-                            d.file_path.includes('__main__.py') ||
-                            d.file_path.includes('cli.py') ||
-                            d.file_path.includes('test_')
-                        );
-                        if (!isEntryPoint) {
-                            return 3; // Thicker red border
-                        }
-                    }
-                    return hasChildren(d) ? 2 : 0;
-                })
-                .style("fill", d => d.color || null);  // Use custom color if available
-
-            // Add rectangles for document nodes
-            node.filter(d => isDocNode(d))
-                .append("rect")
-                .attr("width", d => {
-                    const size = d.complexity ? Math.min(12 + d.complexity * 2, 28) : 15;
-                    return size * 2;
-                })
-                .attr("height", d => {
-                    const size = d.complexity ? Math.min(12 + d.complexity * 2, 28) : 15;
-                    return size * 2;
-                })
-                .attr("x", d => {
-                    const size = d.complexity ? Math.min(12 + d.complexity * 2, 28) : 15;
-                    return -size;
-                })
-                .attr("y", d => {
-                    const size = d.complexity ? Math.min(12 + d.complexity * 2, 28) : 15;
-                    return -size;
-                })
-                .attr("rx", 2)  // Rounded corners
-                .attr("ry", 2)
-                .attr("stroke", d => hasChildren(d) ? "#ffffff" : "none")
-                .attr("stroke-width", d => hasChildren(d) ? 2 : 0)
-                .style("fill", d => d.color || null);
-
-            // Add SVG icons for file and directory nodes
-            node.filter(d => isFileOrDir(d))
-                .append("path")
-                .attr("class", "file-icon")
-                .attr("d", d => getFileTypeIcon(d))
-                .attr("transform", d => {
-                    const scale = d.type === 'directory' ? 1.8 : 1.5;
-                    return `translate(-12, -12) scale(${scale})`;
-                })
-                .style("color", d => getFileTypeColor(d))
-                .attr("stroke", d => hasChildren(d) ? "#ffffff" : "none")
-                .attr("stroke-width", d => hasChildren(d) ? 1 : 0);
-
-            // Add expand/collapse indicator - positioned to the left of label
-            node.filter(d => hasChildren(d))
-                .append("text")
-                .attr("class", "expand-indicator")
-                .attr("x", d => {
-                    const iconRadius = d.type === 'directory' ? 18 : (d.type === 'file' ? 15 : 15);
-                    return iconRadius + 5;  // Just right of the icon (slightly more spacing)
-                })
-                .attr("y", 0)  // Vertically center with icon
-                .attr("dy", "0.6em")  // Fine-tune vertical centering (shifted down)
-                .attr("text-anchor", "start")
-                .style("font-size", "14px")
-                .style("font-weight", "bold")
-                .style("fill", "#ffffff")
-                .style("pointer-events", "none")
-                .text(d => collapsedNodes.has(d.id) ? "+" : "−");
-
-            // Add labels (show actual import statement for L1 nodes)
-            node.append("text")
-                .text(d => {
-                    // L1 (depth 1) nodes are imports
-                    if (d.depth === 1 && d.type !== 'directory' && d.type !== 'file') {
-                        if (d.content) {
-                            // Extract first line of import statement
-                            const importLine = d.content.split('\\n')[0].trim();
-                            // Truncate if too long (max 60 chars)
-                            return importLine.length > 60 ? importLine.substring(0, 57) + '...' : importLine;
-                        }
-                        return d.name;  // Fallback to name if no content
-                    }
-                    return d.name;
-                })
-                .attr("x", d => {
-                    const iconRadius = d.type === 'directory' ? 18 : (d.type === 'file' ? 15 : 15);
-                    const hasExpand = hasChildren(d);
-                    // Position after icon, plus expand indicator width if present (increased spacing)
-                    return iconRadius + 8 + (hasExpand ? 22 : 0);
-                })
-                .attr("y", 0)  // Vertically center with icon
-                .attr("dy", "0.6em")  // Fine-tune vertical centering (shifted down to match expand indicator)
-                .attr("text-anchor", "start");
-
-            simulation.on("tick", () => {
-                link
-                    .attr("x1", d => d.source.x)
-                    .attr("y1", d => d.source.y)
-                    .attr("x2", d => d.target.x)
-                    .attr("y2", d => d.target.y);
-
-                node.attr("transform", d => `translate(${d.x},${d.y})`);
-            });
-
-            updateStats({nodes: visibleNodesList, links: visibleLinks, metadata: {total_files: allNodes.length}});
-        }
-
-        function hasChildren(node) {
-            return allLinks.some(l => (l.source.id || l.source) === node.id);
-        }
-
-        // Zoom to fit all visible nodes
-        function zoomToFit(duration = 750) {
-            const visibleNodesList = allNodes.filter(n => visibleNodes.has(n.id));
-            if (visibleNodesList.length === 0) return;
-
-            // Calculate bounding box of visible nodes
-            const padding = 100;
-            let minX = Infinity, minY = Infinity;
-            let maxX = -Infinity, maxY = -Infinity;
-
-            visibleNodesList.forEach(d => {
-                if (d.x !== undefined && d.y !== undefined) {
-                    minX = Math.min(minX, d.x);
-                    minY = Math.min(minY, d.y);
-                    maxX = Math.max(maxX, d.x);
-                    maxY = Math.max(maxY, d.y);
-                }
-            });
-
-            // Add padding
-            minX -= padding;
-            minY -= padding;
-            maxX += padding;
-            maxY += padding;
-
-            const boxWidth = maxX - minX;
-            const boxHeight = maxY - minY;
-
-            // Calculate scale to fit
-            const scale = Math.min(
-                width / boxWidth,
-                height / boxHeight,
-                2  // Max zoom level
-            ) * 0.9;  // Add 10% margin
-
-            // Calculate center translation
-            const centerX = (minX + maxX) / 2;
-            const centerY = (minY + maxY) / 2;
-            const translateX = width / 2 - scale * centerX;
-            const translateY = height / 2 - scale * centerY;
-
-            // Apply zoom transform with animation
-            svg.transition()
-                .duration(duration)
-                .call(
-                    zoom.transform,
-                    d3.zoomIdentity
-                        .translate(translateX, translateY)
-                        .scale(scale)
-                );
-        }
-
-        function centerNode(node) {
-            // Get current transform to maintain zoom level
-            const transform = d3.zoomTransform(svg.node());
-
-            // Calculate translation to center the node in LEFT portion of viewport
-            // Position at 30% from left to avoid code pane on right side
-            const x = -node.x * transform.k + width * 0.3;
-            const y = -node.y * transform.k + height / 2;
-
-            // Apply smooth animation to center the node
-            svg.transition()
-                .duration(750)
-                .call(zoom.transform, d3.zoomIdentity.translate(x, y).scale(transform.k));
-        }
-
-        function resetView() {
-            // Reset to root level nodes only
-            visibleNodes = new Set(rootNodes.map(n => n.id));
-            collapsedNodes = new Set(rootNodes.map(n => n.id));
-            highlightedNode = null;
-
-            // Re-render graph
-            renderGraph();
-
-            // Zoom to fit after rendering
-            setTimeout(() => {
-                zoomToFit(750);
-            }, 200);
-        }
-
-        function handleNodeClick(event, d) {
-            event.stopPropagation();
-
-            // Always show content pane when clicking any node
-            showContentPane(d);
-
-            // If node has children, also toggle expansion
-            if (hasChildren(d)) {
-                const wasCollapsed = collapsedNodes.has(d.id);
-                if (wasCollapsed) {
-                    expandNode(d);
-                } else {
-                    collapseNode(d);
-                }
-                renderGraph();
-
-                // After rendering and nodes have positions, zoom to fit ONLY visible nodes
-                // Use a small delay to ensure D3 simulation has updated positions
-                if (!wasCollapsed) {
-                    // Wait for simulation to stabilize before zooming
-                    setTimeout(() => {
-                        // Stop simulation to get final positions
-                        simulation.alphaTarget(0);
-                        zoomToFit(750);
-                    }, 200);
-                } else {
-                    // For expansion, center the clicked node after a delay
-                    setTimeout(() => {
-                        centerNode(d);
-                    }, 200);
-                }
-            } else {
-                // For nodes without children, center immediately after a small delay
-                setTimeout(() => {
-                    centerNode(d);
-                }, 100);
-            }
-        }
-
-        function expandNode(node) {
-            collapsedNodes.delete(node.id);
-
-            // Find direct children
-            const children = allLinks
-                .filter(l => (l.source.id || l.source) === node.id)
-                .map(l => allNodes.find(n => n.id === (l.target.id || l.target)))
-                .filter(n => n);
-
-            children.forEach(child => {
-                visibleNodes.add(child.id);
-                collapsedNodes.add(child.id); // Children start collapsed
-            });
-        }
-
-        function collapseNode(node) {
-            collapsedNodes.add(node.id);
-
-            // Hide all descendants recursively
-            function hideDescendants(parentId) {
-                const children = allLinks
-                    .filter(l => (l.source.id || l.source) === parentId)
-                    .map(l => l.target.id || l.target);
-
-                children.forEach(childId => {
-                    visibleNodes.delete(childId);
-                    collapsedNodes.delete(childId);
-                    hideDescendants(childId);
-                });
-            }
-
-            hideDescendants(node.id);
-        }
-
-        function showTooltip(event, d) {
-            // Extract first 2-3 lines of docstring for preview
-            let docPreview = '';
-            if (d.docstring) {
-                const lines = d.docstring.split('\\n').filter(l => l.trim());
-                const previewLines = lines.slice(0, 3).join(' ');
-                const truncated = previewLines.length > 150 ? previewLines.substring(0, 147) + '...' : previewLines;
-                docPreview = `<div style="margin-top: 8px; padding-top: 8px; border-top: 1px solid #30363d; font-size: 11px; color: #8b949e; font-style: italic;">${truncated}</div>`;
-            }
-
-            tooltip
-                .style("display", "block")
-                .style("left", (event.pageX + 10) + "px")
-                .style("top", (event.pageY + 10) + "px")
-                .html(`
-                    <div><strong>${d.name}</strong></div>
-                    <div>Type: ${d.type}</div>
-                    ${d.complexity ? `<div>Complexity: ${d.complexity.toFixed(1)}</div>` : ''}
-                    ${d.start_line ? `<div>Lines: ${d.start_line}-${d.end_line}</div>` : ''}
-                    <div>File: ${d.file_path}</div>
-                    ${docPreview}
-                `);
-        }
-
-        function showLinkTooltip(event, d) {
-            const sourceName = allNodes.find(n => n.id === (d.source.id || d.source))?.name || 'Unknown';
-            const targetName = allNodes.find(n => n.id === (d.target.id || d.target))?.name || 'Unknown';
-
-            // Special tooltip for cycle links
-            if (d.is_cycle) {
-                tooltip
-                    .style("display", "block")
-                    .style("left", (event.pageX + 10) + "px")
-                    .style("top", (event.pageY + 10) + "px")
-                    .html(`
-                        <div style="color: #ff4444;"><strong>⚠️ Circular Dependency Detected</strong></div>
-                        <div style="margin-top: 8px;">Path: ${sourceName} → ${targetName}</div>
-                        <div style="margin-top: 8px; padding-top: 8px; border-top: 1px solid #30363d; font-size: 11px; color: #8b949e; font-style: italic;">
-                            This indicates a circular call relationship that may lead to infinite recursion or tight coupling.
-                        </div>
-                    `);
-                return;
-            }
-
-            // Tooltip content based on link type
-            let typeLabel = '';
-            let typeDescription = '';
-            let extraInfo = '';
-
-            switch(d.type) {
-                case 'caller':
-                    typeLabel = '📞 Function Call';
-                    typeDescription = `${sourceName} calls ${targetName}`;
-                    extraInfo = 'This is a direct function call relationship, the most common type of code dependency.';
-                    break;
-                case 'semantic':
-                    typeLabel = '🔗 Semantic Similarity';
-                    typeDescription = `${(d.similarity * 100).toFixed(1)}% similar`;
-                    extraInfo = `These code chunks have similar meaning or purpose based on their content.`;
-                    break;
-                case 'imports':
-                    typeLabel = '📦 Import Dependency';
-                    typeDescription = `${sourceName} imports ${targetName}`;
-                    extraInfo = 'This is an explicit import/dependency declaration.';
-                    break;
-                case 'file_containment':
-                    typeLabel = '📄 File Contains';
-                    typeDescription = `${sourceName} contains ${targetName}`;
-                    extraInfo = 'This file contains the code chunk or function.';
-                    break;
-                case 'dir_containment':
-                    typeLabel = '📁 Directory Contains';
-                    typeDescription = `${sourceName} contains ${targetName}`;
-                    extraInfo = 'This directory contains the file or subdirectory.';
-                    break;
-                case 'dir_hierarchy':
-                    typeLabel = '🗂️ Directory Hierarchy';
-                    typeDescription = `${sourceName} → ${targetName}`;
-                    extraInfo = 'Parent-child directory structure relationship.';
-                    break;
-                case 'method':
-                    typeLabel = '⚙️ Method Relationship';
-                    typeDescription = `${sourceName} ↔ ${targetName}`;
-                    extraInfo = 'Class method relationship.';
-                    break;
-                case 'module':
-                    typeLabel = '📚 Module Relationship';
-                    typeDescription = `${sourceName} ↔ ${targetName}`;
-                    extraInfo = 'Module-level relationship.';
-                    break;
-                case 'dependency':
-                    typeLabel = '🔀 Dependency';
-                    typeDescription = `${sourceName} depends on ${targetName}`;
-                    extraInfo = 'General code dependency relationship.';
-                    break;
-                default:
-                    typeLabel = `🔗 ${d.type || 'Unknown'}`;
-                    typeDescription = `${sourceName} → ${targetName}`;
-                    extraInfo = 'Code relationship.';
-            }
-
-            tooltip
-                .style("display", "block")
-                .style("left", (event.pageX + 10) + "px")
-                .style("top", (event.pageY + 10) + "px")
-                .html(`
-                    <div><strong>${typeLabel}</strong></div>
-                    <div style="margin-top: 4px;">${typeDescription}</div>
-                    <div style="margin-top: 8px; padding-top: 8px; border-top: 1px solid #30363d; font-size: 11px; color: #8b949e; font-style: italic;">
-                        ${extraInfo}
-                    </div>
-                `);
-        }
-
-        function hideTooltip() {
-            tooltip.style("display", "none");
-        }
-
-        function drag(simulation) {
-            function dragstarted(event) {
-                if (!event.active) simulation.alphaTarget(0.3).restart();
-                event.subject.fx = event.subject.x;
-                event.subject.fy = event.subject.y;
-            }
-
-            function dragged(event) {
-                event.subject.fx = event.x;
-                event.subject.fy = event.y;
-            }
-
-            function dragended(event) {
-                if (!event.active) simulation.alphaTarget(0);
-                event.subject.fx = null;
-                event.subject.fy = null;
-            }
-
-            return d3.drag()
-                .on("start", dragstarted)
-                .on("drag", dragged)
-                .on("end", dragended);
-        }
-
-        function updateStats(data) {
-            const stats = d3.select("#stats");
-            stats.html(`
-                <div>Nodes: ${data.nodes.length}</div>
-                <div>Links: ${data.links.length}</div>
-                ${data.metadata ? `<div>Files: ${data.metadata.total_files || 'N/A'}</div>` : ''}
-                ${data.metadata && data.metadata.is_monorepo ? `<div>Monorepo: ${data.metadata.subprojects.length} subprojects</div>` : ''}
-            `);
-
-            // Show subproject legend if monorepo
-            if (data.metadata && data.metadata.is_monorepo && data.metadata.subprojects.length > 0) {
-                const subprojectsLegend = d3.select("#subprojects-legend");
-                const subprojectsList = d3.select("#subprojects-list");
-
-                subprojectsLegend.style("display", "block");
-
-                // Get subproject nodes with colors
-                const subprojectNodes = allNodes.filter(n => n.type === 'subproject');
-
-                subprojectsList.html(
-                    subprojectNodes.map(sp =>
-                        `<div class="legend-item">
-                            <span class="legend-color" style="background: ${sp.color};"></span> ${sp.name}
-                        </div>`
-                    ).join('')
-                );
-            }
-        }
-
-        function showContentPane(node) {
-            // Highlight the node
-            highlightedNode = node;
-            renderGraph();
-
-            // Populate content pane
-            const pane = document.getElementById('content-pane');
-            const title = document.getElementById('pane-title');
-            const meta = document.getElementById('pane-meta');
-            const content = document.getElementById('pane-content');
-            const footer = document.getElementById('pane-footer');
-
-            // Set title with actual import statement for L1 nodes
-            if (node.depth === 1 && node.type !== 'directory' && node.type !== 'file') {
-                if (node.content) {
-                    const importLine = node.content.split('\\n')[0].trim();
-                    title.textContent = importLine;
-                } else {
-                    title.textContent = `Import: ${node.name}`;
-                }
-            } else {
-                title.textContent = node.name;
-            }
-
-            // Set metadata (type only in header)
-            meta.textContent = node.type;
-
-            // Build footer with annotations
-            let footerHtml = '';
-            if (node.language) {
-                footerHtml += `<span class="footer-item"><span class="footer-label">Language:</span> ${node.language}</span>`;
-            }
-            footerHtml += `<span class="footer-item"><span class="footer-label">File:</span> ${node.file_path}</span>`;
-
-            // Add line information and complexity
-            if (node.start_line !== undefined && node.end_line !== undefined) {
-                const totalLines = node.end_line - node.start_line + 1;
-
-                if (node.type === 'function' || node.type === 'class' || node.type === 'method') {
-                    // For functions/classes: show function lines
-                    footerHtml += `<span class="footer-item"><span class="footer-label">Lines:</span> ${node.start_line}-${node.end_line} (${totalLines} lines)</span>`;
-                } else if (node.type === 'file') {
-                    // For files: show file lines
-                    footerHtml += `<span class="footer-item"><span class="footer-label">File Lines:</span> ${totalLines}</span>`;
-                } else {
-                    // For other types: show location
-                    footerHtml += `<span class="footer-item"><span class="footer-label">Location:</span> Lines ${node.start_line}-${node.end_line}</span>`;
-                }
-
-                // Add cyclomatic complexity if available and > 0
-                if (node.complexity && node.complexity > 0) {
-                    footerHtml += `<span class="footer-item"><span class="footer-label">Complexity:</span> ${node.complexity}</span>`;
-                }
-            }
-
-            footer.innerHTML = footerHtml;
-
-            // Display content based on node type
-            if (node.type === 'directory') {
-                showDirectoryContents(node, content, footer);
-            } else if (node.type === 'file') {
-                showFileContents(node, content);
-            } else if (node.depth === 1 && node.type !== 'directory' && node.type !== 'file') {
-                // L1 nodes are imports
-                showImportDetails(node, content);
-            } else {
-                // Class, function, method, code nodes
-                showCodeContent(node, content);
-            }
-
-            pane.classList.add('visible');
-        }
-
-        function showDirectoryContents(node, container, footer) {
-            // Find all direct children of this directory
-            const children = allLinks
-                .filter(l => (l.source.id || l.source) === node.id)
-                .map(l => allNodes.find(n => n.id === (l.target.id || l.target)))
-                .filter(n => n);
-
-            if (children.length === 0) {
-                container.innerHTML = '<p style="color: #8b949e;">Empty directory</p>';
-                // Update footer with file path only
-                footer.innerHTML = `<span class="footer-item"><span class="footer-label">File:</span> ${node.file_path}</span>`;
-                return;
-            }
-
-            // Group by type
-            const files = children.filter(n => n.type === 'file');
-            const subdirs = children.filter(n => n.type === 'directory');
-            const chunks = children.filter(n => n.type !== 'file' && n.type !== 'directory');
-
-            let html = '<ul class="directory-list">';
-
-            // Show subdirectories first
-            subdirs.forEach(child => {
-                html += `
-                    <li data-node-id="${child.id}">
-                        <span class="item-icon">📁</span>
-                        ${child.name}
-                    </li>
-                `;
-            });
-
-            // Then files
-            files.forEach(child => {
-                html += `
-                    <li data-node-id="${child.id}">
-                        <span class="item-icon">📄</span>
-                        ${child.name}
-                    </li>
-                `;
-            });
-
-            // Then code chunks
-            chunks.forEach(child => {
-                const icon = child.type === 'class' ? '🔷' : child.type === 'function' ? '⚡' : '📝';
-                html += `
-                    <li data-node-id="${child.id}">
-                        <span class="item-icon">${icon}</span>
-                        ${child.name}
-                    </li>
-                `;
-            });
-
-            html += '</ul>';
-
-            container.innerHTML = html;
-
-            // Add click handlers to list items
-            const listItems = container.querySelectorAll('.directory-list li');
-            listItems.forEach(item => {
-                item.addEventListener('click', () => {
-                    const nodeId = item.getAttribute('data-node-id');
-                    const childNode = allNodes.find(n => n.id === nodeId);
-                    if (childNode) {
-                        showContentPane(childNode);
-                    }
-                });
-            });
-
-            // Update footer with file path and summary
-            footer.innerHTML = `
-                <span class="footer-item"><span class="footer-label">File:</span> ${node.file_path}</span>
-                <span class="footer-item"><span class="footer-label">Total:</span> ${children.length} items (${subdirs.length} directories, ${files.length} files, ${chunks.length} code chunks)</span>
-            `;
-        }
-
-        function showFileContents(node, container) {
-            // Find all chunks in this file
-            const fileChunks = allLinks
-                .filter(l => (l.source.id || l.source) === node.id)
-                .map(l => allNodes.find(n => n.id === (l.target.id || l.target)))
-                .filter(n => n);
-
-            if (fileChunks.length === 0) {
-                container.innerHTML = '<p style="color: #8b949e;">No code chunks found in this file</p>';
-                return;
-            }
-
-            // Collect all content from chunks and sort by line number
-            const sortedChunks = fileChunks
-                .filter(c => c.content)
-                .sort((a, b) => a.start_line - b.start_line);
-
-            if (sortedChunks.length === 0) {
-                container.innerHTML = '<p style="color: #8b949e;">File content not available</p>';
-                return;
-            }
-
-            // Combine all chunks to show full file
-            const fullContent = sortedChunks.map(c => c.content).join('\\n\\n');
-
-            container.innerHTML = `
-                <p style="color: #8b949e; font-size: 11px; margin-bottom: 12px;">
-                    Contains ${fileChunks.length} code chunks
-                </p>
-                <pre><code>${escapeHtml(fullContent)}</code></pre>
-            `;
-        }
-
-        function showImportDetails(node, container) {
-            // L1 nodes are import statements - show import content prominently
-            // Note: File, Location, and Language are now in the footer
-            const importHtml = `
-                <div class="import-details">
-                    ${node.content ? `
-                        <div style="margin-bottom: 16px;">
-                            <div class="detail-label" style="margin-bottom: 8px;">Import Statement:</div>
-                            <pre><code>${escapeHtml(node.content)}</code></pre>
-                        </div>
-                    ` : '<p style="color: #8b949e;">No import content available</p>'}
-                </div>
-            `;
-
-            container.innerHTML = importHtml;
-        }
-
-        // Parse docstring sections (Args, Returns, Raises, etc.)
-        function parseDocstring(docstring) {
-            if (!docstring) return { brief: '', sections: {} };
-
-            const lines = docstring.split('\\n');
-            const sections = {};
-            let currentSection = 'brief';
-            let currentContent = [];
-
-            for (let line of lines) {
-                const trimmed = line.trim();
-                // Check for section headers (Args:, Returns:, Raises:, etc.)
-                const sectionMatch = trimmed.match(/^(Args?|Returns?|Yields?|Raises?|Note|Notes|Example|Examples|See Also|Docs?|Parameters?):?$/i);
-
-                if (sectionMatch) {
-                    // Save previous section
-                    if (currentContent.length > 0) {
-                        sections[currentSection] = currentContent.join('\\n').trim();
-                    }
-                    // Start new section
-                    currentSection = sectionMatch[1].toLowerCase();
-                    currentContent = [];
-                } else {
-                    currentContent.push(line);
-                }
-            }
-
-            // Save last section
-            if (currentContent.length > 0) {
-                sections[currentSection] = currentContent.join('\\n').trim();
-            }
-
-            return { brief: sections.brief || '', sections };
-        }
-
-        function showCodeContent(node, container) {
-            // Show code for function, class, method, or code chunks
-            let html = '';
-
-            // Parse docstring to extract sections
-            const docInfo = parseDocstring(node.docstring);
-
-            // Show brief description (non-sectioned part) in content area
-            if (docInfo.brief && docInfo.brief.trim()) {
-                html += `
-                    <div style="margin-bottom: 16px; padding: 12px; background: #161b22; border: 1px solid #30363d; border-radius: 6px;">
-                        <div style="font-size: 11px; color: #8b949e; margin-bottom: 8px; font-weight: 600;">DESCRIPTION</div>
-                        <pre style="margin: 0; padding: 0; background: transparent; border: none; white-space: pre-wrap;"><code>${escapeHtml(docInfo.brief)}</code></pre>
-                    </div>
-                `;
-            }
-
-            if (node.content) {
-                html += `<pre><code>${escapeHtml(node.content)}</code></pre>`;
-            } else {
-                html += '<p style="color: #8b949e;">No content available</p>';
-            }
-
-            container.innerHTML = html;
-
-            // Update footer with docstring sections
-            const footer = document.getElementById('pane-footer');
-            let footerHtml = '';
-
-            // Add existing footer items
-            if (node.language) {
-                footerHtml += `<div class="footer-item"><span class="footer-label">Language:</span> <span class="footer-value">${node.language}</span></div>`;
-            }
-            footerHtml += `<div class="footer-item"><span class="footer-label">File:</span> <span class="footer-value">${node.file_path}</span></div>`;
-            if (node.start_line) {
-                footerHtml += `<div class="footer-item"><span class="footer-label">Lines:</span> <span class="footer-value">${node.start_line}-${node.end_line}</span></div>`;
-            }
-
-            // Add "Called By" section for external callers
-            if (node.callers && node.callers.length > 0) {
-                footerHtml += `<div class="footer-item" style="margin-top: 8px; padding-top: 8px; border-top: 1px solid #30363d;">`;
-                footerHtml += `<span class="footer-label">Called By:</span><br/>`;
-                node.callers.forEach(caller => {
-                    const fileName = caller.file.split('/').pop();
-                    const callerDisplay = `${fileName}::${caller.name}`;
-                    footerHtml += `<span class="footer-value" style="display: block; margin-left: 8px; margin-top: 4px;">
-                        <a href="#" class="caller-link" data-chunk-id="${caller.chunk_id}" style="color: #58a6ff; text-decoration: none; cursor: pointer;">
-                            • ${escapeHtml(callerDisplay)}
-                        </a>
-                    </span>`;
-                });
-                footerHtml += `</div>`;
-            } else if (node.type === 'function' || node.type === 'method' || node.type === 'class') {
-                // Only show "no callers" message for callable entities
-                footerHtml += `<div class="footer-item" style="margin-top: 8px; padding-top: 8px; border-top: 1px solid #30363d;">`;
-                footerHtml += `<span class="footer-label">Called By:</span> <span class="footer-value" style="font-style: italic; color: #6e7681;">(No external callers found)</span>`;
-                footerHtml += `</div>`;
-            }
-
-            // Add docstring sections to footer
-            const sectionLabels = {
-                'docs': 'Docs',
-                'doc': 'Docs',
-                'args': 'Args',
-                'arg': 'Args',
-                'parameters': 'Args',
-                'parameter': 'Args',
-                'returns': 'Returns',
-                'return': 'Returns',
-                'yields': 'Yields',
-                'yield': 'Yields',
-                'raises': 'Raises',
-                'raise': 'Raises',
-                'note': 'Note',
-                'notes': 'Note',
-                'example': 'Example',
-                'examples': 'Example',
-            };
-
-            for (let [key, content] of Object.entries(docInfo.sections)) {
-                if (key === 'brief') continue; // Already shown above
-
-                const label = sectionLabels[key] || key.charAt(0).toUpperCase() + key.slice(1);
-                // Truncate long sections for footer
-                const truncated = content.length > 200 ? content.substring(0, 197) + '...' : content;
-
-                footerHtml += `<div class="footer-item"><span class="footer-label">${label}:</span> <span class="footer-value">${escapeHtml(truncated)}</span></div>`;
-            }
-
-            footer.innerHTML = footerHtml;
-
-            // Add click handlers to caller links
-            const callerLinks = footer.querySelectorAll('.caller-link');
-            callerLinks.forEach(link => {
-                link.addEventListener('click', (e) => {
-                    e.preventDefault();
-                    const chunkId = link.getAttribute('data-chunk-id');
-                    const callerNode = allNodes.find(n => n.id === chunkId);
-                    if (callerNode) {
-                        // Navigate to the caller node
-                        navigateToNode(callerNode);
-                    }
-                });
-            });
-        }
-
-        function escapeHtml(text) {
-            const div = document.createElement('div');
-            div.textContent = text;
-            return div.innerHTML;
-        }
-
-        function navigateToNode(targetNode) {
-            // Ensure the node is visible in the graph
-            if (!visibleNodes.has(targetNode.id)) {
-                // Expand parent nodes to make this node visible
-                expandParentsToNode(targetNode);
-                renderGraph();
-            }
-
-            // Show the content pane for this node
-            showContentPane(targetNode);
-
-            // Zoom to the target node
-            setTimeout(() => {
-                // Find the node's position
-                if (targetNode.x !== undefined && targetNode.y !== undefined) {
-                    const scale = 1.5;  // Zoom level
-                    // Position at 30% from left to avoid code pane on right side
-                    const translateX = width * 0.3 - scale * targetNode.x;
-                    const translateY = height / 2 - scale * targetNode.y;
-
-                    svg.transition()
-                        .duration(750)
-                        .call(
-                            zoom.transform,
-                            d3.zoomIdentity
-                                .translate(translateX, translateY)
-                                .scale(scale)
-                        );
-                }
-            }, 200);
-        }
-
-        function expandParentsToNode(targetNode) {
-            // Build a path from root to target node
-            const path = [];
-            let current = targetNode;
-
-            while (current) {
-                path.unshift(current);
-                // Find parent
-                const parentLink = allLinks.find(l =>
-                    (l.target.id || l.target) === current.id &&
-                    (l.type !== 'semantic' && l.type !== 'dependency')
-                );
-                if (parentLink) {
-                    const parentId = parentLink.source.id || parentLink.source;
-                    current = allNodes.find(n => n.id === parentId);
-                } else {
-                    break;
-                }
-            }
-
-            // Expand all nodes in the path
-            path.forEach(node => {
-                if (!visibleNodes.has(node.id)) {
-                    visibleNodes.add(node.id);
-                }
-                if (collapsedNodes.has(node.id)) {
-                    expandNode(node);
-                }
-            });
-        }
-
-        function closeContentPane() {
-            const pane = document.getElementById('content-pane');
-            pane.classList.remove('visible');
-
-            // Remove highlight
-            highlightedNode = null;
-            renderGraph();
-        }
-
-        // Auto-load graph data on page load with progress tracking
-        window.addEventListener('DOMContentLoaded', () => {
-            const loadingEl = document.getElementById('loading');
-
-            // Show initial loading message
-            loadingEl.innerHTML = '<label style="color: #58a6ff;"><span class="spinner"></span>Loading graph data...</label><br>' +
-                                 '<div style="margin-top: 8px; background: #21262d; border-radius: 4px; height: 20px; width: 250px; position: relative; overflow: hidden;">' +
-                                 '<div id="progress-bar" style="background: #238636; height: 100%; width: 0%; transition: width 0.3s;"></div>' +
-                                 '</div>' +
-                                 '<small id="progress-text" style="color: #8b949e; margin-top: 4px; display: block;">Connecting...</small>';
-
-            // Create abort controller for timeout
-            const controller = new AbortController();
-            const timeout = setTimeout(() => controller.abort(), 60000); // 60s timeout for large files
-
-            fetch("chunk-graph.json", { signal: controller.signal })
-                .then(response => {
-                    if (!response.ok) {
-                        throw new Error(`HTTP ${response.status}: ${response.statusText}`);
-                    }
-
-                    const contentLength = response.headers.get('content-length');
-                    const total = contentLength ? parseInt(contentLength, 10) : 0;
-                    let loaded = 0;
-
-                    const progressBar = document.getElementById('progress-bar');
-                    const progressText = document.getElementById('progress-text');
-
-                    // Update progress text based on file size
-                    if (total > 0) {
-                        const sizeMB = (total / (1024 * 1024)).toFixed(1);
-                        progressText.textContent = `Downloading ${sizeMB}MB...`;
-                    } else {
-                        progressText.textContent = 'Downloading...';
-                    }
-
-                    // Create a new response with progress tracking
-                    const reader = response.body.getReader();
-                    const stream = new ReadableStream({
-                        start(controller) {
-                            function push() {
-                                reader.read().then(({ done, value }) => {
-                                    if (done) {
-                                        controller.close();
-                                        return;
-                                    }
-
-                                    loaded += value.byteLength;
-
-                                    // Update progress bar
-                                    if (total > 0) {
-                                        const percent = Math.round((loaded / total) * 100);
-                                        progressBar.style.width = percent + '%';
-                                        const loadedMB = (loaded / (1024 * 1024)).toFixed(1);
-                                        const totalMB = (total / (1024 * 1024)).toFixed(1);
-                                        progressText.textContent = `Downloaded ${loadedMB}MB / ${totalMB}MB (${percent}%)`;
-                                    } else {
-                                        const loadedMB = (loaded / (1024 * 1024)).toFixed(1);
-                                        progressText.textContent = `Downloaded ${loadedMB}MB...`;
-                                    }
-
-                                    controller.enqueue(value);
-                                    push();
-                                }).catch(err => {
-                                    console.error('Stream reading error:', err);
-                                    controller.error(err);
-                                });
-                            }
-                            push();
-                        }
-                    });
-
-                    return new Response(stream);
-                })
-                .then(response => {
-                    clearTimeout(timeout);
-
-                    // Update UI for parsing phase
-                    const progressText = document.getElementById('progress-text');
-                    const progressBar = document.getElementById('progress-bar');
-                    progressBar.style.width = '100%';
-                    progressText.textContent = 'Parsing JSON data...';
-
-                    // Parse JSON (this may take time for large files)
-                    return response.json();
-                })
-                .then(data => {
-                    clearTimeout(timeout);
-                    loadingEl.innerHTML = '<label style="color: #238636;">✓ Graph loaded successfully</label>';
-                    setTimeout(() => loadingEl.style.display = 'none', 2000);
-                    visualizeGraph(data);
-                })
-                .catch(err => {
-                    clearTimeout(timeout);
-
-                    let errorMsg = err.message;
-                    if (err.name === 'AbortError') {
-                        errorMsg = 'Loading timeout - file may be too large or server unresponsive';
-                    }
-
-                    loadingEl.innerHTML = `<label style="color: #f85149;">✗ Failed to load graph data</label><br>` +
-                                         `<small style="color: #8b949e;">${errorMsg}</small><br>` +
-                                         `<small style="color: #8b949e;">Run: mcp-vector-search visualize export</small>`;
-                    console.error("Failed to load graph:", err);
-                });
-        });
-
-        // Reset view button event handler
-        document.getElementById('reset-view-btn').addEventListener('click', () => {
-            resetView();
-        });
-    </script>
-</body>
-</html>"""
-
-    with open(html_file, "w") as f:
-        f.write(html_content)