codegraphcontext 0.5.2__py3-none-any.whl → 0.5.3__py3-none-any.whl

codegraphcontext/cli/main.py

@@ -25,6 +25,7 @@ from importlib.metadata import version as pkg_version, PackageNotFoundError
 from codegraphcontext.server import MCPServer
 from .setup_wizard import run_neo4j_setup_wizard, configure_mcp_client
 from . import config_manager
+from . import project_config
 # Import the new helper functions
 from .cli_helpers import (
     index_helper,
@@ -82,6 +83,8 @@ app = typer.Typer(
     name="cgc",
     help="CodeGraphContext: An MCP server for AI-powered code analysis.",
     add_completion=True,
+    # `-h` is accepted as --help on every command, not just at the root.
+    context_settings={"help_option_names": ["-h", "--help"]},
 )
 console = Console(stderr=True)
 
@@ -576,7 +579,7 @@ def config_reset():
         console.print("[yellow]Reset cancelled[/yellow]")
 
 @config_app.command("db")
-def config_db(backend: str = typer.Argument(..., help="Database backend: 'neo4j', 'falkordb', 'falkordb-remote', 'kuzudb', or 'ladybugdb'")):
+def config_db(backend: str = typer.Argument(..., help="Database backend: 'neo4j', 'falkordb', 'falkordb-remote', 'kuzudb', 'nornic', or 'ladybugdb'")):
     """
     Quickly switch the default database backend.
     
@@ -588,9 +591,9 @@ def config_db(backend: str = typer.Argument(..., help="Database backend: 'neo4j'
         cgc config db kuzudb
     """
     backend = backend.lower()
-    if backend not in ['falkordb', 'falkordb-remote', 'neo4j', 'kuzudb', 'ladybugdb']:
+    if backend not in ['falkordb', 'falkordb-remote', 'neo4j', 'kuzudb', 'nornic', 'ladybugdb']:
         console.print(f"[bold red]Invalid backend: {backend}[/bold red]")
-        console.print("Must be 'falkordb', 'falkordb-remote', 'neo4j', 'kuzudb', or 'ladybugdb'")
+        console.print("Must be 'falkordb', 'falkordb-remote', 'neo4j', 'kuzudb', 'nornic', or 'ladybugdb'")
         raise typer.Exit(code=1)
     
     updated = config_manager.set_config_value("DEFAULT_DATABASE", backend)
@@ -600,6 +603,99 @@ def config_db(backend: str = typer.Argument(..., help="Database backend: 'neo4j'
 
     console.print(f"[green]✔ Default database switched to {backend}[/green]")
 
+# ============================================================================
+# PROMPT COMMAND GROUP - Custom LLM Prompts
+# ============================================================================
+
+prompt_app = typer.Typer(help="Manage custom LLM prompt files")
+app.add_typer(prompt_app, name="prompt")
+
+@prompt_app.command("add")
+def prompt_add(
+    path: str = typer.Argument(..., help="Path to the prompt file to register")
+):
+    """
+    Add a custom prompt file to the project.
+    
+    Registers a prompt file that will be injected into the LLM system prompt.
+    The file path is stored relative to the project root.
+    
+    Examples:
+        cgc prompt add skills.md
+        cgc prompt add docs/custom-instructions.txt
+        cgc prompt add /absolute/path/to/prompt.md
+    """
+    try:
+        success = project_config.add_prompt_file(path)
+        if not success:
+            raise typer.Exit(code=1)
+    except Exception as e:
+        console.print(f"[red]Error adding prompt file: {e}[/red]")
+        raise typer.Exit(code=1)
+
+@prompt_app.command("list")
+def prompt_list():
+    """
+    List all registered prompt files.
+    
+    Shows all custom prompt files that will be injected into the LLM system prompt.
+    Files are shown in the order they will be prepended.
+    """
+    try:
+        prompts = project_config.list_prompt_files()
+        
+        if not prompts:
+            console.print("[yellow]No custom prompt files registered.[/yellow]")
+            console.print("\nUse [cyan]cgc prompt add <path>[/cyan] to register a prompt file.")
+            return
+        
+        console.print("[bold cyan]Registered Prompt Files:[/bold cyan]\n")
+        
+        table = Table(show_header=True, header_style="bold magenta")
+        table.add_column("#", style="dim", width=3)
+        table.add_column("Path", style="green")
+        table.add_column("Status", style="cyan", width=10)
+        
+        project_root = project_config.get_project_root()
+        for i, prompt_path in enumerate(prompts, 1):
+            # Check if file exists
+            prompt_file = Path(prompt_path)
+            if not prompt_file.is_absolute():
+                prompt_file = project_root / prompt_file
+            
+            status = "✅ Found" if prompt_file.exists() else "⚠️ Missing"
+            table.add_row(str(i), prompt_path, status)
+        
+        console.print(table)
+        
+        config_file = project_config.get_project_config_file()
+        console.print(f"\n[dim]Config: {config_file}[/dim]")
+        
+    except Exception as e:
+        console.print(f"[red]Error listing prompt files: {e}[/red]")
+        raise typer.Exit(code=1)
+
+@prompt_app.command("remove")
+def prompt_remove(
+    path: str = typer.Argument(..., help="Path to the prompt file to unregister")
+):
+    """
+    Remove a custom prompt file from the project.
+    
+    Unregisters a prompt file so it will no longer be injected into the LLM system prompt.
+    
+    Examples:
+        cgc prompt remove skills.md
+        cgc prompt remove docs/custom-instructions.txt
+    """
+    try:
+        success = project_config.remove_prompt_file(path)
+        if not success:
+            raise typer.Exit(code=1)
+    except Exception as e:
+        console.print(f"[red]Error removing prompt file: {e}[/red]")
+        raise typer.Exit(code=1)
+
 # ============================================================================
 # BUNDLE COMMAND GROUP - Pre-indexed Graph Snapshots
 # ============================================================================
@@ -735,6 +831,7 @@ def bundle_load(
     bundle_name: str = typer.Argument(..., help="Bundle name or path to load (e.g., 'numpy' or 'numpy.cgc')"),
     clear: bool = typer.Option(False, "--clear", help="Clear existing graph data before loading"),
     yes: bool = typer.Option(False, "--yes", "-y", help="Skip confirmation when using --clear"),
+    context: Optional[str] = typer.Option(None, "--context", "-c", help="Specific context to use"),
 ):
     """
     Load a pre-indexed bundle (download if needed, then import).
@@ -755,7 +852,7 @@ def bundle_load(
     
     # If it's an absolute path or has .cgc extension and exists, use it directly
     if bundle_path.is_absolute() or (bundle_path.suffix == '.cgc' and bundle_path.exists()):
-        bundle_import(str(bundle_path), clear=clear, yes=yes)
+        bundle_import(str(bundle_path), clear=clear, yes=yes, context=context)
         return
     
     # Add .cgc extension if not present
@@ -765,7 +862,7 @@ def bundle_load(
     # Check if exists locally
     if bundle_path.exists():
         console.print(f"[dim]Found local bundle: {bundle_path}[/dim]")
-        bundle_import(str(bundle_path), clear=clear, yes=yes)
+        bundle_import(str(bundle_path), clear=clear, yes=yes, context=context)
         return
     
     # Try to download from registry
@@ -783,7 +880,7 @@ def bundle_load(
         
         if downloaded_path:
             # Import the downloaded bundle
-            bundle_import(downloaded_path, clear=clear, yes=yes)
+            bundle_import(downloaded_path, clear=clear, yes=yes, context=context)
         else:
             console.print(f"[bold red]Failed to download bundle '{name}'[/bold red]")
             raise typer.Exit(code=1)
@@ -921,9 +1018,12 @@ def load_shortcut(
     bundle_name: str = typer.Argument(..., help="Bundle name or path to load"),
     clear: bool = typer.Option(False, "--clear", help="Clear existing graph data before loading"),
     yes: bool = typer.Option(False, "--yes", "-y", help="Skip confirmation when using --clear"),
+    context: Optional[str] = typer.Option(None, "--context", "-c", help="Specific context to use"),
 ):
     """Shortcut for 'cgc bundle load'"""
-    bundle_load(bundle_name, clear, yes=yes)
+    # Must pass `context` explicitly: invoked as a plain function, Typer does not
+    # resolve defaults, so an omitted parameter keeps its OptionInfo sentinel.
+    bundle_load(bundle_name, clear, yes=yes, context=context)
 
 # ============================================================================
 # REGISTRY COMMAND GROUP - Browse and Download Bundles
@@ -1024,7 +1124,7 @@ def registry_download(
     
     if load and bundle_path:
         console.print("\n[cyan]Loading bundle...[/cyan]")
-        bundle_import(bundle_path, clear=False)
+        bundle_import(bundle_path, clear=False, yes=False, context=None)
 
 @registry_app.command("request")
 def registry_request(
@@ -1063,6 +1163,10 @@ def doctor():
     console.print("[bold cyan]🏥 Running CodeGraphContext Diagnostics...[/bold cyan]\n")
     
     all_checks_passed = True
+    # Warnings are not failures, but printing "All diagnostics passed! System is
+    # healthy." while a ⚠ is on screen is misleading — `doctor` is the command
+    # people run when something is already wrong.
+    warnings_found = False
 
     config_manager.ensure_first_run_bootstrap()
     config_manager.ensure_config_file()
@@ -1200,6 +1304,32 @@ def doctor():
 
                 if is_falkordb_usable():
                     console.print("   [green]✓[/green] FalkorDB Lite is installed")
+                    # An import probe is not a connection check. This section is
+                    # titled "Checking Database Connection" and the neo4j /
+                    # falkordb-remote branches genuinely connect, so the default
+                    # backend must too — otherwise `doctor` reports a healthy
+                    # system without ever touching the database.
+                    try:
+                        from codegraphcontext.core import get_database_manager
+
+                        probe_manager = get_database_manager()
+                        try:
+                            with probe_manager.get_driver().session() as probe_session:
+                                probe_session.run("RETURN 1")
+                            console.print("   [green]✓[/green] FalkorDB Lite connection successful")
+                            backend_in_use = probe_manager.get_backend_type()
+                            if backend_in_use != "falkordb":
+                                console.print(
+                                    f"   [yellow]⚠[/yellow] Configured backend is 'falkordb' but "
+                                    f"'{backend_in_use}' is actually active"
+                                )
+                                warnings_found = True
+                        finally:
+                            probe_manager.close_driver()
+                    except Exception as conn_error:
+                        console.print("   [red]✗[/red] FalkorDB Lite connection failed")
+                        console.print(f"       Reason: {conn_error}")
+                        all_checks_passed = False
                 else:
                     raise ImportError("FalkorDB Lite is not available on this platform")
             except ImportError:
@@ -1210,6 +1340,7 @@ def doctor():
                 all_checks_passed = False
         else:
             console.print(f"   [yellow]⚠[/yellow] No connectivity probe for backend '{default_db}'")
+            warnings_found = True
     except Exception as e:
         console.print(f"   [red]✗[/red] Database check error: {e}")
         all_checks_passed = False
@@ -1239,6 +1370,7 @@ def doctor():
             console.print(f"   [green]✓[/green] {len(available)}/{len(probe_langs)} probed parsers OK: {', '.join(available)}")
             if unavailable:
                 console.print(f"   [yellow]⚠[/yellow] Unavailable: {', '.join(unavailable)}")
+                warnings_found = True
         except ImportError:
             console.print("   [red]✗[/red] tree-sitter-language-pack not installed")
             all_checks_passed = False
@@ -1264,6 +1396,7 @@ def doctor():
                 all_checks_passed = False
         else:
             console.print("   [yellow]⚠[/yellow] Config directory doesn't exist, will be created on first use")
+            warnings_found = True
     except Exception as e:
         console.print(f"   [red]✗[/red] Permission check error: {e}")
         all_checks_passed = False
@@ -1276,11 +1409,17 @@ def doctor():
         console.print(f"   [green]✓[/green] cgc command found at: {cgc_path}")
     else:
         console.print("   [yellow]⚠[/yellow] cgc command not in PATH (using python -m cgc)")
+        warnings_found = True
     
     # Final summary
     console.print("\n" + "=" * 60)
-    if all_checks_passed:
+    if all_checks_passed and not warnings_found:
         console.print("[bold green]✅ All diagnostics passed! System is healthy.[/bold green]")
+    elif all_checks_passed:
+        console.print(
+            "[bold yellow]✅ No failures, but some checks reported warnings "
+            "(⚠ above).[/bold yellow]"
+        )
     else:
         console.print("[bold yellow]⚠️  Some issues detected. Please review the output above.[/bold yellow]")
         console.print("\n[cyan]Common fixes:[/cyan]")
@@ -1295,7 +1434,6 @@ def doctor():
 
 
 
-@app.command()
 @app.command()
 def index(
     path: Optional[str] = typer.Argument(None, help="Path to the directory or file to index. Defaults to the current directory."),
@@ -1320,9 +1458,18 @@ def index(
             reindex_helper(path, context)
         else:
             index_helper(path, context)
+    except typer.Exit:
+        # typer.Exit subclasses RuntimeError and str() is empty, so the handler
+        # below caught it, printed nothing, and returned 0 — every helper that
+        # raised `typer.Exit(code=1)` (missing path, failed indexing) silently
+        # became a success. Re-raise control flow before catching errors.
+        raise
     except Exception as e:
         if str(e):
             console.print(f"[red]An error occurred during indexing: {e}[/red]")
+        else:
+            console.print("[red]An error occurred during indexing.[/red]")
+        raise typer.Exit(code=1)
 
     if summarize:
         import os
@@ -1411,6 +1558,7 @@ def setup_scip():
 def delete(
     path: Optional[str] = typer.Argument(None, help="Path of the repository to delete from the code graph."),
     all_repos: bool = typer.Option(False, "--all", help="Delete all indexed repositories"),
+    yes: bool = typer.Option(False, "--yes", "-y", help="Skip the confirmation prompt (for CI/non-interactive use)"),
     context: Optional[str] = typer.Option(None, "--context", "-c", help="Specific context to use")
 ):
     """
@@ -1508,6 +1656,22 @@ def delete(
             )
             raise typer.Exit(code=1)
 
+        # `--all` demands a typer.confirm *and* typing "delete all", while a
+        # single delete went straight through — irreversibly dropping a
+        # repository's entire graph (potentially an hour of indexing) on a
+        # typo, with no prompt, no --yes flag and no undo. The asymmetry was
+        # actively misleading: anyone who had seen the heavy --all guardrails
+        # would reasonably assume single deletes were guarded too.
+        if not yes:
+            resolved = Path(path).expanduser().resolve()
+            console.print(
+                f"[bold yellow]About to delete the graph for:[/bold yellow] {resolved}"
+            )
+            console.print("[dim]This is irreversible; re-indexing is the only way back.[/dim]")
+            if not typer.confirm("Proceed?", default=False):
+                console.print("[yellow]Deletion cancelled.[/yellow]")
+                raise typer.Exit(code=1)
+
         delete_helper(path, context)
 
 
@@ -1515,6 +1679,7 @@ def delete(
 def report(
     output: Optional[str] = typer.Option(None, "--output", "-o", help="Output file path. Defaults to CGC_REPORT.md in the current directory."),
     java: bool = typer.Option(False, "--java", "-j", help="Include Spring/Maven Java sections."),
+    repo: Optional[str] = typer.Option(None, "--repo", "-r", help="Repository root to scope the report to. Defaults to auto-detection from the current directory."),
     context: Optional[str] = typer.Option(None, "--context", "-c", help="Specific context to use"),
 ):
     """
@@ -1533,7 +1698,15 @@ def report(
     db_manager, _, _, _ = _initialize_services(context)
     try:
         from codegraphcontext.tools.report_generator import generate_report
-        report_text = generate_report(db_manager, output_path=output_path, include_java=java)
+        # Without --repo the generator silently picks the repo with the most
+        # indexed files, which is disclosed only in the report body.
+        scoped_repo = Path(repo).expanduser().resolve().as_posix() if repo else None
+        report_text = generate_report(
+            db_manager,
+            output_path=output_path,
+            include_java=java,
+            repo_path=scoped_repo,
+        )
         console.print(f"[green]✓[/green] Report written to [bold]{output_path}[/bold]")
         # Print a short preview (first ~40 lines)
         preview_lines = report_text.splitlines()[:40]
@@ -1553,7 +1726,9 @@ def report(
 @app.command()
 def visualize(
     repo: Optional[str] = typer.Option(None, "--repo", "-r", help="Path to the repository to visualize."),
-    host: str = typer.Option("127.0.0.1", "--host", "-h", help="Host interface to bind to."),
+    # `-h` is --help everywhere else in the CLI; use -H so `cgc visualize -h`
+    # doesn't fail with "Option '-h' requires an argument".
+    host: str = typer.Option("127.0.0.1", "--host", "-H", help="Host interface to bind to."),
     port: int = typer.Option(8000, "--port", "-p", help="Port to run the visualizer server on."),
     context: Optional[str] = typer.Option(None, "--context", "-c", help="Specific context to use")
 ):
@@ -1642,7 +1817,11 @@ def unwatch(
     context: Optional[str] = typer.Option(None, "--context", "-c", help="Specific context to use"),
 ):
     """
-    Stop watching a directory for changes.
+    [MCP only] Stop watching a directory for changes.
+
+    Not supported from the CLI: this cannot reach a watcher running in another
+    process. Press Ctrl+C in the 'cgc watch' terminal, or use the
+    'unwatch_directory' MCP tool.
     
     Note: This command is primarily for MCP server mode.
     For CLI watch mode, simply press Ctrl+C in the watch terminal.
@@ -1658,7 +1837,10 @@ def watching(
     context: Optional[str] = typer.Option(None, "--context", "-c", help="Specific context to use"),
 ):
     """
-    List all directories currently being watched for changes.
+    [MCP only] List all directories currently being watched for changes.
+
+    Not supported from the CLI: this cannot reach a watcher running in another
+    process. Use the 'list_watched_paths' MCP tool.
     
     Note: This command is primarily for MCP server mode.
     For CLI watch mode, check the terminal where you ran 'cgc watch'.
@@ -2867,10 +3049,13 @@ def cypher_legacy(
 def index_abbrev(
     path: Optional[str] = typer.Argument(None, help="Path to index"),
     force: bool = typer.Option(False, "--force", "-f", help="Force re-index (delete existing and rebuild)"),
+    summarize: bool = typer.Option(False, "--summarize", "-s", help="Display a codebase summary after indexing"),
     context: Optional[str] = typer.Option(None, "--context", "-c", help="Specific context to use")
 ):
     """Shortcut for 'cgc index'"""
-    index(path, force=force, context=context)
+    # `summarize` must be passed explicitly: omitted, it keeps its OptionInfo
+    # sentinel, which is truthy — so `cgc i` always printed the summary.
+    index(path, force=force, summarize=summarize, context=context)
 
 @app.command("ls", rich_help_panel="Shortcuts")
 def list_abbrev(
@@ -2883,10 +3068,13 @@ def list_abbrev(
 def delete_abbrev(
     path: Optional[str] = typer.Argument(None, help="Path to delete"),
     all_repos: bool = typer.Option(False, "--all", help="Delete all indexed repositories"),
+    yes: bool = typer.Option(False, "--yes", "-y", help="Skip the confirmation prompt (for CI/non-interactive use)"),
     context: Optional[str] = typer.Option(None, "--context", "-c", help="Specific context to use")
 ):
     """Shortcut for 'cgc delete'"""
-    delete(path, all_repos, context=context)
+    # `yes` must be forwarded explicitly: omitted, it keeps its OptionInfo
+    # sentinel, which is truthy — silently skipping the confirmation.
+    delete(path, all_repos, yes=yes, context=context)
 
 @app.command("v", rich_help_panel="Shortcuts")
 def visualize_abbrev(
@@ -3161,5 +3349,9 @@ def _write_datasource_graph(ingested: dict, context: Optional[str] = None) -> No
         db_manager.close_driver()
 
 
+from codegraphcontext.cli.simulator import simulate_app
+app.add_typer(simulate_app, name="simulate")
+
+
 if __name__ == "__main__":
     app()

codegraphcontext/cli/project_config.py

@@ -0,0 +1,218 @@
+"""
+Project-level configuration management for CodeGraphContext.
+Handles managing .cgc directory and project-specific settings like custom prompts.
+"""
+
+import json
+import logging
+from pathlib import Path
+from typing import List, Optional, Dict, Any
+from rich.console import Console
+
+console = Console()
+logger = logging.getLogger(__name__)
+
+# Project config directory and file
+PROJECT_CONFIG_DIR_NAME = ".cgc"
+PROJECT_CONFIG_FILE_NAME = "config.json"
+
+
+def get_project_root() -> Path:
+    """Get the current working directory as project root."""
+    return Path.cwd()
+
+
+def get_project_config_dir(project_root: Optional[Path] = None) -> Path:
+    """Get the .cgc directory path for the project."""
+    if project_root is None:
+        project_root = get_project_root()
+    return project_root / PROJECT_CONFIG_DIR_NAME
+
+
+def get_project_config_file(project_root: Optional[Path] = None) -> Path:
+    """Get the config.json file path within .cgc directory."""
+    return get_project_config_dir(project_root) / PROJECT_CONFIG_FILE_NAME
+
+
+def ensure_project_config_dir(project_root: Optional[Path] = None) -> Path:
+    """Ensure .cgc directory exists and return its path."""
+    config_dir = get_project_config_dir(project_root)
+    config_dir.mkdir(parents=True, exist_ok=True)
+    return config_dir
+
+
+def load_project_config(project_root: Optional[Path] = None) -> Dict[str, Any]:
+    """
+    Load project configuration from .cgc/config.json.
+    Returns an empty config structure if file doesn't exist.
+    """
+    config_file = get_project_config_file(project_root)
+    
+    if not config_file.exists():
+        return {"prompts": []}
+    
+    try:
+        with open(config_file, "r", encoding="utf-8") as f:
+            config = json.load(f)
+            # Ensure prompts field exists
+            if "prompts" not in config:
+                config["prompts"] = []
+            return config
+    except json.JSONDecodeError as e:
+        console.print(f"[yellow]Warning: Invalid JSON in {config_file}: {e}[/yellow]")
+        return {"prompts": []}
+    except Exception as e:
+        console.print(f"[yellow]Warning: Could not load config: {e}[/yellow]")
+        return {"prompts": []}
+
+
+def save_project_config(config: Dict[str, Any], project_root: Optional[Path] = None):
+    """Save project configuration to .cgc/config.json."""
+    ensure_project_config_dir(project_root)
+    config_file = get_project_config_file(project_root)
+    
+    try:
+        with open(config_file, "w", encoding="utf-8") as f:
+            json.dump(config, f, indent=2)
+    except Exception as e:
+        console.print(f"[red]Error saving project config: {e}[/red]")
+        raise
+
+
+def add_prompt_file(prompt_path: str, project_root: Optional[Path] = None) -> bool:
+    """
+    Add a custom prompt file to the project configuration.
+    Validates that the file exists and prevents duplicates.
+    Stores paths relative to project root.
+    
+    Returns True if successful, False otherwise.
+    """
+    if project_root is None:
+        project_root = get_project_root()
+    
+    # Convert to Path object and resolve
+    prompt_file = Path(prompt_path)
+    
+    # Check if file exists
+    if not prompt_file.exists():
+        console.print(f"[red]❌ File not found: {prompt_path}[/red]")
+        return False
+    
+    if not prompt_file.is_file():
+        console.print(f"[red]❌ Not a file: {prompt_path}[/red]")
+        return False
+    
+    # Make path relative to project root if it's absolute and within project
+    try:
+        if prompt_file.is_absolute():
+            try:
+                relative_path = prompt_file.relative_to(project_root)
+                prompt_path_str = str(relative_path).replace("\\", "/")
+            except ValueError:
+                # File is outside project root, store as absolute
+                prompt_path_str = str(prompt_file.resolve()).replace("\\", "/")
+        else:
+            prompt_path_str = str(prompt_file).replace("\\", "/")
+    except Exception:
+        prompt_path_str = str(prompt_file).replace("\\", "/")
+    
+    # Load current config
+    config = load_project_config(project_root)
+    
+    # Check for duplicates
+    if prompt_path_str in config["prompts"]:
+        console.print(f"[yellow]⚠ Prompt file already registered: {prompt_path_str}[/yellow]")
+        return False
+    
+    # Add to config
+    config["prompts"].append(prompt_path_str)
+    save_project_config(config, project_root)
+    
+    console.print(f"[green]✅ Added prompt file: {prompt_path_str}[/green]")
+    return True
+
+
+def list_prompt_files(project_root: Optional[Path] = None) -> List[str]:
+    """
+    Get list of registered prompt files.
+    Returns list of prompt file paths.
+    """
+    config = load_project_config(project_root)
+    return config.get("prompts", [])
+
+
+def remove_prompt_file(prompt_path: str, project_root: Optional[Path] = None) -> bool:
+    """
+    Remove a prompt file from the project configuration.
+    
+    Returns True if successful, False otherwise.
+    """
+    if project_root is None:
+        project_root = get_project_root()
+    
+    # Normalize the path for comparison
+    prompt_file = Path(prompt_path)
+    
+    # Try both relative and absolute versions
+    try:
+        if prompt_file.is_absolute():
+            try:
+                relative_path = prompt_file.relative_to(project_root)
+                prompt_path_normalized = str(relative_path).replace("\\", "/")
+            except ValueError:
+                prompt_path_normalized = str(prompt_file.resolve()).replace("\\", "/")
+        else:
+            prompt_path_normalized = str(prompt_file).replace("\\", "/")
+    except Exception:
+        prompt_path_normalized = str(prompt_file).replace("\\", "/")
+    
+    # Load current config
+    config = load_project_config(project_root)
+    
+    # Try to remove - check both the normalized path and original
+    original_length = len(config["prompts"])
+    config["prompts"] = [p for p in config["prompts"] if p not in (prompt_path, prompt_path_normalized)]
+    
+    if len(config["prompts"]) == original_length:
+        console.print(f"[yellow]⚠ Prompt file not found in config: {prompt_path}[/yellow]")
+        return False
+    
+    save_project_config(config, project_root)
+    console.print(f"[green]✅ Removed prompt file: {prompt_path}[/green]")
+    return True
+
+
+def get_prompt_file_contents(project_root: Optional[Path] = None) -> List[str]:
+    """
+    Load contents of all registered prompt files.
+    Skips files that don't exist and logs warnings.
+    
+    Returns list of prompt file contents in order.
+    """
+    if project_root is None:
+        project_root = get_project_root()
+    
+    prompt_files = list_prompt_files(project_root)
+    contents = []
+    
+    for prompt_path in prompt_files:
+        # Resolve path relative to project root
+        prompt_file = Path(prompt_path)
+        if not prompt_file.is_absolute():
+            prompt_file = project_root / prompt_file
+        
+        # Try to read file
+        try:
+            if not prompt_file.exists():
+                logger.warning(f"Skipping missing prompt file: {prompt_path}")
+                continue
+            
+            with open(prompt_file, "r", encoding="utf-8") as f:
+                content = f.read().strip()
+                if content:
+                    contents.append(content)
+        except Exception as e:
+            logger.warning(f"Error reading prompt file {prompt_path}: {e}")
+            continue
+    
+    return contents

codegraphcontext/cli/registry_commands.py

@@ -112,7 +112,7 @@ def list_bundles(verbose: bool = False, unique: bool = False):
         table.add_column("Download URL", style="blue", no_wrap=False)
     
     # Sort by full_name to group versions together
-    bundles.sort(key=lambda b: (b.get('name', ''), b.get('full_name', '')))
+    bundles.sort(key=lambda b: ((b.get('name') or ''), (b.get('full_name') or '')))
     
     for bundle in bundles:
         # Use full_name for display (includes version info)
@@ -163,10 +163,10 @@ def search_bundles(query: str):
     query_lower = query.lower()
     matching_bundles = [
         b for b in bundles
-        if query_lower in b.get('name', '').lower() or
-           query_lower in b.get('full_name', '').lower() or
-           query_lower in b.get('repo', '').lower() or
-           query_lower in b.get('description', '').lower()
+        if query_lower in (b.get('name') or '').lower() or
+           query_lower in (b.get('full_name') or '').lower() or
+           query_lower in (b.get('repo') or '').lower() or
+           query_lower in (b.get('description') or '').lower()
     ]
     
     if not matching_bundles:
@@ -407,7 +407,7 @@ def load_bundle_command(bundle_name: str, clear_existing: bool = False):
         if not all(services):
             return (False, "Failed to initialize database services", {})
         
-        db_manager, _, _ = services
+        db_manager, _, _, _ = services
         
         # Check if bundle exists locally
         bundle_path = Path(bundle_name)