feat: Add cgc prompt command for custom LLM prompts (#583) by DhineshPonnarasan · Pull Request #613 · CodeGraphContext/CodeGraphContext

DhineshPonnarasan · 2026-02-08T08:53:44Z

Summary

Implements #583 - Adds a new cgc prompt CLI command that allows users to register custom LLM prompt files that are injected into the system prompt at runtime.

Features

New CLI command group: cgc prompt with subcommands:
cgc prompt add <path> - Register a custom prompt file
cgc prompt list - List all registered prompts with status
cgc prompt remove <path> - Unregister a prompt file
Project-level configuration stored in .cgc/config.json
Paths stored as relative paths (when within project)
File validation and duplicate prevention
Custom prompts prepended to base system prompt at MCP server initialization
Missing files at runtime are skipped with warnings (no crashes)
Full backward compatibility - works exactly as before when no prompts configured

Implementation Details

Created project_config.py module for managing .cgc/config.json
Added build_system_prompt() function to dynamically load and combine prompts
Integrated with MCP server initialization to inject custom prompts
Uses proper logging patterns for runtime warnings

Testing

All CLI commands tested and working
Config persistence verified
File validation working correctly
Multiple prompts load in correct order
Missing file handling works without crashes
Backward compatibility verified (no breaking changes)
MCP server initialization tested with custom prompts

Screenshots:

…GraphContext#583) - Add new 'cgc prompt' CLI command group with add/list/remove subcommands - Create project_config.py module for managing .cgc/config.json - Store custom prompt paths in project-level config (relative paths) - Implement build_system_prompt() to prepend custom prompts at runtime - Integrate with MCP server initialization to inject custom prompts - Add file validation, duplicate prevention, and missing file handling - Maintain full backward compatibility when no prompts are configured - Use proper logging for runtime warnings Changes: - src/codegraphcontext/cli/project_config.py (new) - src/codegraphcontext/cli/main.py (add prompt command group) - src/codegraphcontext/prompts.py (add build_system_prompt function) - src/codegraphcontext/server.py (use build_system_prompt in initialize) Resolves CodeGraphContext#583

vercel · 2026-02-08T08:53:49Z

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Pull request overview

Adds support for project-specific “custom system prompts” by introducing a new cgc prompt CLI command group, persisting prompt file registrations in a per-project config, and injecting those prompt files into the MCP server’s system prompt during initialization.

Changes:

Add cgc prompt add|list|remove commands to manage registered prompt files.
Introduce .cgc/config.json project config handling for storing prompt paths and loading file contents.
Update MCP server initialization to use a dynamically-built system prompt that prepends custom prompts.

Reviewed changes

Copilot reviewed 4 out of 5 changed files in this pull request and generated 6 comments.

Show a summary per file

File	Description
website/package-lock.json	Lockfile updates (adds `peer: true` metadata on several entries).
src/codegraphcontext/server.py	Switches MCP initialize response to use `build_system_prompt()` output.
src/codegraphcontext/prompts.py	Adds `build_system_prompt()` to prepend custom prompt file contents to `LLM_SYSTEM_PROMPT`.
src/codegraphcontext/cli/project_config.py	New module for `.cgc/config.json` management and prompt file registration/loading.
src/codegraphcontext/cli/main.py	Adds `cgc prompt` Typer subcommands wired to `project_config`.

Files not reviewed (1)

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Copilot · 2026-02-08T08:57:09Z

src/codegraphcontext/cli/project_config.py

+from rich.console import Console
+
+console = Console()
+logger = logging.getLogger(__name__)


project_config is imported at MCP server init via build_system_prompt(). Using Console() (default stdout) risks writing to stdout (e.g., warnings/errors) and breaking the JSON-RPC protocol, since the server uses stdout for responses. Prefer removing console output from this module (use logger.*) or at minimum configure Console(stderr=True) and ensure all non-JSON output goes to stderr.

Copilot · 2026-02-08T08:57:10Z

src/codegraphcontext/cli/project_config.py

+    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": []}


These console.print(...) warnings in config loading can end up on stdout when called from the MCP server, corrupting JSON-RPC output. Switch these to logger.warning(...) (optionally with exc_info=True) or print explicitly to stderr.

Copilot · 2026-02-08T08:57:10Z

src/codegraphcontext/cli/project_config.py

+    # 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


Duplicate prevention is currently string-based (prompt_path_str in config["prompts"]), so paths like skills.md vs ./skills.md (or differing case on Windows) can be registered multiple times. Normalize to a canonical form (e.g., resolve() then relative_to(project_root) when possible, and consistent slash/case normalization) before storing and comparing.

Copilot · 2026-02-08T08:57:10Z

src/codegraphcontext/cli/main.py

+# ============================================================================
+# PROMPT COMMAND GROUP - Custom LLM Prompts
+# ============================================================================
+
+prompt_app = typer.Typer(help="Manage custom LLM prompt files")
+app.add_typer(prompt_app, name="prompt")
+


New cgc prompt commands introduce user-facing behavior (config persistence, relative path handling, duplicate detection, missing-file status). Add CLI tests (e.g., Typer CliRunner) to cover prompt add/list/remove and verify .cgc/config.json contents and exit codes.

Copilot · 2026-02-08T08:57:10Z

src/codegraphcontext/prompts.py

+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.
+    """


build_system_prompt() now has non-trivial logic (loading config, reading multiple files, ordering/formatting, and fallback behavior on missing/invalid configs). Add unit tests for: no config, config with multiple prompts, missing prompt files (skipped), invalid JSON config (does not crash / no stdout), and preservation of base prompt.

Copilot · 2026-02-08T08:57:11Z

src/codegraphcontext/prompts.py

+    # 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)
+


build_system_prompt() pulls get_prompt_file_contents from codegraphcontext.cli.project_config, which couples prompt construction (used by the MCP server) to the CLI layer and its Rich console side effects. Consider moving the project config reader into a non-CLI module (or make it side-effect-free) so the server can import it without bringing in CLI concerns or risking stdout writes.

Shashankss1205 · 2026-02-08T09:01:51Z

I dont understand why is this so complex?

We just needed to add prompts.py file in the config and retrieve it from there. Perhaps there's a confusion?

DhineshPonnarasan · 2026-02-08T09:13:10Z

Thank you for the feedback! I want to make sure I understand the requirement correctly.

What I implemented:

CLI commands (cgc prompt add/list/remove) to manage custom prompt files
Store paths in .cgc/config.json
Load and inject custom prompts into the LLM system prompt

Your feedback suggests a simpler approach. Could you clarify:

What was the original requirement in issue New tool/cli cmd #583? (I want to see the exact issue text to ensure I understand correctly)
What approach did you have in mind? For example:

Option A: Store a single path in config → {"custom_prompt_path": "path/to/file.md"}
Option B: Store the prompt text directly in config → {"custom_prompt": "text here..."}
Option C: Something else?

Should there be CLI commands at all, or should users just manually edit the config file?

I'm happy to simplify the implementation once I understand the expected approach

Copilot AI review requested due to automatic review settings February 8, 2026 08:53

Copilot started reviewing on behalf of DhineshPonnarasan February 8, 2026 08:54 View session

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feat: Add cgc prompt command for custom LLM prompts (#583)#613

feat: Add cgc prompt command for custom LLM prompts (#583)#613
DhineshPonnarasan wants to merge 1 commit intoCodeGraphContext:mainfrom
DhineshPonnarasan:feature/cgc-prompt-command

DhineshPonnarasan commented Feb 8, 2026 •

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DhineshPonnarasan commented Feb 8, 2026 •

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