What is codebase-RAG CLAUDE.md?

Project instructions for a codebase search system, also called retrieval-augmented generation, that lets an AI find and understand functions in a repository using ordinary language. It describes setup, running the server, indexing files, and testing.

Use it when setting up or developing the codebase search server, starting its MCP connection, performing full or incremental indexing, and running its tests.

It gives an agent the commands and project structure needed to work on the repository without guessing. It also explains how to refresh the search index when code changes.

How bluewings1211/codebase-RAG configures Claude Code

Reuse

Borrowing it

Nothing to install: this file belongs to bluewings1211/codebase-RAG. Take a copy, put it at the same path in your own repository, and replace the rules that are about this project with yours.

Copy the file

curl -O https://raw.githubusercontent.com/bluewings1211/codebase-RAG/dev/CLAUDE.md

Clone the repo

git clone --depth 1 https://github.com/bluewings1211/codebase-RAG

Made for: Claude Code.

Wrote this? Show the measurements

A badge with what this costs and how it scanned, read live from this page, so it follows the numbers instead of freezing them. Markdown for a README, HTML for a documentation site or a project page.

README.md

[![agentmods](https://agentmods.dev/badge/instructions/bluewings1211/codebase-rag/claude-md/github.svg)](https://agentmods.dev/instructions/bluewings1211/codebase-rag/claude-md)

Your own site

<a href="https://agentmods.dev/instructions/bluewings1211/codebase-rag/claude-md"><img src="https://agentmods.dev/badge/instructions/bluewings1211/codebase-rag/claude-md/github.svg" alt="Measured on agentmods" height="20"></a>

Or the 80×15 button, for a site that already has a row of RSS and ATOM ones. Only the verdict fits; the numbers stay here.

Your own site · 80×15

<a href="https://agentmods.dev/instructions/bluewings1211/codebase-rag/claude-md"><img src="https://agentmods.dev/badge/instructions/bluewings1211/codebase-rag/claude-md.svg" alt="Reviewed on agentmods" width="80" height="20"></a>

Per session 1,675 This file is loaded in full into every session.

When invoked 1,675 The same file — it is already loaded in full.

Security scan A 0 findings. A grade says what 26 rules found in the file — not that it is safe.

Origin original No closer match found in the catalogue.

Token cost

What it costs to keep this loaded

Counted locally with the o200k_base tokenizer, which is exact for GPT models; Claude uses its own tokenizer and its counts differ. Treat this as one consistent yardstick across the catalogue rather than a bill. Prices are per million input tokens.

Model	Per session	Once invoked
Fable 5.1	$0.01675	$0.01675
Opus 5.5	$0.00670	$0.00670
Sonnet 5.5	$0.00335	$0.00335
Haiku 4.5	$0.00168	$0.00168

Measured 2mo ago against content hash 0604ba24f0fc, method: parsed. Prices are Anthropic first-party input rates as of 2026-10-07, from the pricing page.

Security

Grade A, and why

codebase-RAG CLAUDE.md scanned grade A with 0 findings against 26 rules in 11 categories — prompt injection, anti-refusal, data exfiltration, privilege escalation, supply chain, agent snooping, system-prompt leakage, SSRF and excessive agency — measured 2mo ago.

A static scan of the body, not an audit. Every finding is printed with the line that produced it so you can judge whether it matters here. A mod is markdown that instructs an agent; that is exactly why what it instructs is worth reading.

Nothing flagged

None of the 26 patterns this scan looks for appear in this file: no shell pipes, no recursive deletes, no credential paths, no hidden text, no instruction-override or anti-refusal phrasing, no agent-config snooping. That is not a guarantee, it is the absence of the things that are checkable.

CLAUDE.md · 160 lines

How it starts

The opening of the file, as written. The whole thing — 160 lines — stays where its author put it; the contents beside it link to each section on GitHub.

CLAUDE.md

This file provides guidance to Claude Code (claude.ai/code) when working with code in this repository.

Development Commands

# Setup and Installation
./setup.sh                          # Run setup script

# Run MCP Server
uv run python src/run_mcp.py        # Start MCP server

# Manual Indexing
uv run python manual_indexing.py -d "." -m clear_existing    # Full reindex
uv run python manual_indexing.py -d "." -m incremental       # Incremental update

# Testing
uv run pytest src/tests/            # Run tests

Architecture Overview

This is a Codebase RAG (Retrieval-Augmented Generation) MCP Server that enables AI agents to understand and query codebases using natural language with function-level precision through intelligent syntax-aware code chunking.

Project Structure

src/
├── main.py                    # MCP server entry point
├── run_mcp.py                 # Server startup script
├── models/                    # Data models and structures
│   ├── code_chunk.py         # Intelligent chunk representations
│   └── file_metadata.py      # File tracking and metadata
├── services/                  # Core business logic
│   ├── code_parser_service.py    # AST parsing and chunking
│   ├── indexing_service.py       # Orchestration and processing
│   ├── embedding_service.py      # Ollama integration
│   ├── reranker_service.py       # Cross-encoder reranking (Two-Stage RAG)
│   ├── qdrant_service.py         # Vector database operations
│   └── project_analysis_service.py # Repository analysis
├── tools/                     # MCP tool implementations
│   ├── core/                 # Error handling and utilities
│   ├── indexing/             # Parsing and chunking tools
│   └── project/              # Project management tools
├── utils/                     # Shared utilities
│   ├── logging_config.py        # Centralized logging with file rotation
│   ├── language_registry.py     # Language support definitions
│   ├── tree_sitter_manager.py   # Parser management
│   └── performance_monitor.py   # Progress tracking
└── prompts/                   # Advanced query prompts (future)

Root Files:
├── manual_indexing.py         # Standalone indexing tool
├── pyproject.toml            # uv/Python configuration
└── docs/                     # Documentation (referenced)

Read the full file on GitHub · 160 lines

Changes

What this file has done since we first saw it

Hashed on every crawl. A supply-chain change to an agent config is a question of when, not whether, so the history is kept rather than the latest state alone.

2mo ago First seen · 160 lines · 1,675 tokens per session scan A 0604ba24f0fc

Subscribe to this mod's changes

codebase-RAG CLAUDE.md is an instructions file published in the GitHub repository bluewings1211/codebase-RAG (15 stars, last pushed 11mo ago), licensed MIT. It adds 1,675 tokens to every session, about $0.0067 per session on Opus 5.5. A static security scan graded it A with 0 findings. No closer match exists in the catalogue, so it is treated as the original; first seen 2026-08-30.

Data and AI RAG and vectors mcp-server retrival-augmented-generation

codebase-RAG CLAUDE.md next to 6 instructions from other repositories
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codebase-RAG: Instructions file for Claude Code