Shashankss1205 · Jul 26, 2026 · Feb 8, 2026 · Jul 26, 2026 · Jul 26, 2026
diff --git a/src/codegraphcontext/cli/main.py b/src/codegraphcontext/cli/main.py
@@ -25,6 +25,7 @@
 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,
@@ -600,6 +601,99 @@ 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
 # ============================================================================

diff --git a/src/codegraphcontext/cli/project_config.py b/src/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
diff --git a/src/codegraphcontext/prompts.py b/src/codegraphcontext/prompts.py
@@ -6,6 +6,12 @@
 provided by this MCP server.
 """
 
+from pathlib import Path
+from typing import Optional
+import logging
+
+logger = logging.getLogger(__name__)
+
 LLM_SYSTEM_PROMPT = """# AI Pair Programmer Instructions
 
 ## 1. Your Role and Goal
@@ -122,4 +128,48 @@
 2.  **Identify Failure:** If the standard tools cannot answer a complex, multi-step relationship query (e.g., "Find all functions that are called by a method in a class that inherits from 'BaseHandler'"), then and only then, resort to the fallback.
 3.  **Formulate & Execute:** Construct a Cypher query to find the answer and execute it using `execute_cypher_query`. **Consult the Graph Schema Reference above to ensure you use the correct property names (e.g. `path` vs `path`).**
 4.  **Present Results:** Explain the results to the user based on the query output.
-"""
+"""
+
+
+def build_system_prompt(project_root: Optional[Path] = None) -> str:
+    """
+    Build the complete system prompt by prepending custom prompt files.
+
+    Args:
+        project_root: Root directory of the project. If None, uses current directory.
+
+    Returns:
+        Complete system prompt with custom prompts prepended to the base prompt.
+    """
+    # Import here to avoid circular dependencies
+    try:
+        from codegraphcontext.cli.project_config import get_prompt_file_contents
+
+        # Get custom prompt contents
+        custom_prompts = get_prompt_file_contents(project_root)
+
+        if not custom_prompts:
+            # No custom prompts, return base prompt
+            return LLM_SYSTEM_PROMPT
+
+        # Build combined prompt: custom prompts first, then base prompt
+        combined_parts = []
+
+        # Add custom prompts
+        for i, custom_content in enumerate(custom_prompts, 1):
+            combined_parts.append(f"# Custom Instructions {i}\n\n{custom_content}")
+
+        # Add separator and base prompt
+        combined_parts.append("---\n")
+        combined_parts.append(LLM_SYSTEM_PROMPT)
+
+        return "\n\n".join(combined_parts)
+
+    except ImportError:
+        # If project_config is not available (shouldn't happen in normal use)
+        logger.warning("Could not import project_config module, using base prompt only")
+        return LLM_SYSTEM_PROMPT
+    except Exception as e:
+        # Log error but continue with base prompt to maintain backward compatibility
+        logger.warning(f"Error loading custom prompts: {e}. Using base prompt only.")
+        return LLM_SYSTEM_PROMPT