codebase-intel MCP server

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AI coding agents can autocomplete, refactor, and generate code. But they still fail at the things that matter most in production:

• They don't know your team decided to use token bucket over sliding window — and why
• They don't know the compliance team requires rate limit headers on every response
• They don't know that changing config.py will break billing and analytics
• They generate code that looks right but violates your project's architectural patterns

codebase-intel fixes this. It's the context layer that sits between your codebase and any AI agent — providing not just what code exists, but why it exists, what rules it must follow, and what breaks if you change it.

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Before vs After

WITHOUT codebase-intel                    WITH codebase-intel
─────────────────────                     ───────────────────

Agent reads: every file in the dir        Agent reads: only what matters
Tokens used: 16,063                       Tokens used: 5,955
Knows why code exists: No                 Knows why: Yes (13 decisions)
Quality guardrails: None                  Guardrails: 4 contracts enforced
Drift awareness: None                     Drift: stale context detected
Impact analysis: None                     Impact: knows what else breaks

Result: faster but fragile                Result: faster AND correct

Real benchmarks on production codebases

Project	Files	Naive Tokens	codebase-intel	Reduction	Decisions	Contracts
FastAPI monolith (auth + frontend)	359	16,063	5,955	63%	13	4
Microservice A (AI processing)	358	14,611	5,955	59%	0	7
Microservice B (document generation)	87	2,461	1,275	48%	0	6
Microservice C (user management)	153	5,904	1,476	75%	0	4

Numbers from codebase-intel benchmark on real production repos. The token reduction comes from targeted graph traversal. The decisions and contracts are what no other tool provides.

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What makes this different

There are great tools for code graphs (code-review-graph is excellent — 6K+ stars). We don't compete with them. We solve what they don't:

Capability	Graph-only tools	codebase-intel
Code graph + dependencies	Yes	Yes (19 languages)
Decision Journal — why code is the way it is	No	Yes
Quality Contracts — rules AI must follow	No	Yes
AI Anti-pattern Detection — catches hallucinated imports, over-abstraction	No	Yes
Drift Detection — stale context, context rot alerts	No	Yes
Token Budgeting — fits context to any agent's window	No	Yes
Live Analytics — prove efficiency over time	No	Yes

The missing layer

What exists today:          What codebase-intel adds:

Code → Graph → Agent        Code → Graph ──────────────────→ Agent
                                     ↓                         ↑
                              Decision Journal ──→ WHY ────────┤
                              Quality Contracts → RULES ───────┤
                              Drift Detector ──→ WARNINGS ─────┘
                              
                              "Here are the 3 files that matter,
                               the decision your team made 6 months ago,
                               and the 2 rules you must not violate."

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Quick Start

# Install globally (no venv needed)
uvx codebase-intel --help          # ephemeral, like npx
# or
pipx install codebase-intel        # persistent global install
# or
pip install codebase-intel         # traditional

# Initialize on your project
cd your-project
codebase-intel init

# See what it found
codebase-intel status

# Mine decisions from git history
codebase-intel mine --save

# Auto-detect code patterns and generate quality contracts
codebase-intel detect-patterns --save

# Run benchmarks (see the before/after)
codebase-intel benchmark

# View live dashboard
codebase-intel dashboard

Connect to Claude Code / any MCP client

Single project:

{
  "mcpServers": {
    "codebase-intel": {
      "command": "codebase-intel",
      "args": ["serve", "/path/to/your/project"]
    }
  }
}

Multiple projects (global mode):

# Register repos once from anywhere
codebase-intel register ~/projects/user-service
codebase-intel register /opt/services/payment-api
codebase-intel register /var/repos/notification-service

{
  "mcpServers": {
    "codebase-intel": {
      "command": "uvx",
      "args": ["codebase-intel", "serve", "--auto"]
    }
  }
}

In --auto mode, the MCP server automatically routes each request to the correct project based on file paths in the request. No manual switching — works like npx @playwright/mcp.

Now your agent automatically gets relevant context, decisions, and contracts before writing code.

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The Three Pillars

1. Decision Journal — "Why does this code exist?"

Every team makes hundreds of decisions that never get documented. Why did you choose Postgres over Mongo? Why is auth middleware structured that way? Why was the sliding window approach rejected?

codebase-intel captures these from git history automatically and links them to code:

# .codebase-intel/decisions/DEC-042.yaml
id: DEC-042
title: "Use token bucket for rate limiting"
status: active
context: "Payment endpoint was getting hammered during flash sales"
decision: "Token bucket algorithm with per-user buckets, 100 req/min"
alternatives:
  - name: sliding_window
    rejection_reason: "Memory overhead too high at scale"
constraints:
  - description: "Must not add >2ms p99 latency"
    source: sla
    is_hard: true
code_anchors:
  - "src/middleware/rate_limiter.py:15-82"

Without this: your agent proposes sliding window (the exact approach you rejected 6 months ago). With this: your agent sees the decision, follows it, and respects the SLA constraint.

2. Quality Contracts — "What rules must AI follow?"

Linters check syntax. Contracts enforce your project's patterns:

# .codebase-intel/contracts/api-rules.yaml
rules:
  - id: no-raw-sql
    name: No raw SQL in API layer
    severity: error
    pattern: "execute\\(.*SELECT|INSERT|UPDATE"
    fix_suggestion: "Use the repository pattern"

  - id: async-everywhere
    name: All I/O must be async
    severity: error
    pattern: "requests\\.(get|post)"
    fix_suggestion: "Use httpx.AsyncClient"

Built-in AI guardrails catch the patterns AI agents mess up most:

• Hallucinated imports (modules that don't exist)
• Over-abstraction (base classes with one subclass)
• Unnecessary error handling for impossible conditions
• Comments that restate code instead of explaining why
• Features that weren't requested (YAGNI violations)

3. Drift Detection — "Is our context still valid?"

Context rots. Decisions get outdated. Code anchors point to deleted files. codebase-intel detects this:

$ codebase-intel drift

╭──────────────── Drift Report ────────────────╮
│ Overall: MEDIUM                               │
│ 3 items need attention                        │
╰───────────────────────────────────────────────╯

- [MEDIUM] Decision DEC-012 anchored to deleted file
- [MEDIUM] Decision DEC-008 is past its review date
- [LOW] 2 files changed since last graph index

---

19 Languages

Full tree-sitter parsing via tree-sitter-language-pack:

Category	Languages
Web	JavaScript, TypeScript, TSX
Backend	Python, Java, Go, Ruby, PHP, Elixir
Systems	Rust, C, C++
Mobile	Swift, Kotlin, Dart
Other	C#, Scala, Lua, Haskell

---

CLI Commands

# Core
codebase-intel init [path]              # Initialize — build graph, create configs
codebase-intel analyze [--incremental]  # Rebuild or update the code graph
codebase-intel mine [--save]            # Mine git history for decision candidates
codebase-intel detect-patterns [--save] # Auto-detect code patterns → quality contracts
codebase-intel drift                    # Run drift detection
codebase-intel benchmark                # Measure token efficiency (before/after)
codebase-intel dashboard                # Live efficiency tracking over time
codebase-intel serve [path]             # Start MCP server (single project)
codebase-intel status                   # Component health check
codebase-intel intent [--verify]        # Track and verify delivery goals

# Global workspace (multi-project)
codebase-intel register <path>          # Register a project globally
codebase-intel unregister <id>          # Remove from global registry
codebase-intel projects                 # List all registered projects
codebase-intel serve --auto             # Start MCP server for ALL registered projects

# Cross-repo (microservices)
codebase-intel crossrepo <paths...>     # Scan repos for cross-service dependencies
codebase-intel crossrepo --all          # Scan all registered projects

# Intent graph (v0.3)
codebase-intel why "<title>" "<reason>" -f <file>   # Record a why (confirmed trust)
codebase-intel install-hooks            # Install the pre-commit intent gate
codebase-intel intent-gate              # Run the gate manually
codebase-intel intent-check             # Repair moved anchors, flag drift, report coverage
codebase-intel intent-confirm <node-id> # Promote an agent-asserted why to confirmed
codebase-intel intent-render -f html -o intent.html  # Human view (html | mermaid)
codebase-intel intent-migrate           # Import v1 decisions into the intent graph
codebase-intel intent-rebuild           # Rebuild the SQLite index from the journal
codebase-intel intent-eval [repos...]   # Token + correctness A/B vs the v1 baseline

MCP Tools (16 tools)

Tool	What it does
get_context	The main tool. Assembles relevant files + decisions + contracts within a token budget.
query_graph	Query dependencies, dependents, or run impact analysis.
get_decisions	Get architectural decisions relevant to specific files.
get_contracts	Get quality contracts for files you're editing.
check_drift	Verify context freshness before trusting old decisions.
impact_analysis	"What breaks if I change this file?"
get_status	Health check — graph stats, decision count, contract count.
record_feedback	Record if AI output was accepted/rejected — powers the learning loop.
get_efficiency_report	Live token savings, acceptance rate, before/after proof.
set_intent	Capture what the user wants with machine-verifiable acceptance criteria.
check_intent	Verify if acceptance criteria are actually met before marking done.
list_intents	Show all tracked intents with completion status.
bootstrap	Call first in a session. System orientation + task-relevant whys, packed into a token budget.
check_precedent	Was this already decided — or decided and reversed? Call before structural choices.
record_why	Record why a structural decision was made, at the moment it's made.
get_intent	Traverse the intent graph by node, file, or abstraction level; no args = coverage stats.

---

Community Contract Packs

Pre-built quality rules for popular frameworks:

Pack	Rules	Covers
fastapi.yaml	10	Layered architecture, Pydantic schemas, async, Depends(), secrets
react-typescript.yaml	11	Functional components, no any, custom hooks, lazy loading
nodejs-express.yaml	12	Error handling, helmet, rate limiting, structured logging

cp community-contracts/fastapi.yaml .codebase-intel/contracts/

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New in v0.3.0 — the Intent Graph

v0.2 could tell an agent what decisions exist. v0.3 captures why at the moment a decision is made, and lets agents traverse that reasoning instead of re-reading files and re-deciding things that were already decided.

• Journal-first. .codebase-intel/intent-journal/*.jsonl is the committed source of truth; intent-graph.db is a derived, git-ignored index you can always rebuild (intent-rebuild).
• Four abstraction levels — system topology → service/module → component/flow → function/decision — linked with parent/child and supersedes edges.
• Trust tiers, surfaced everywhere: mined (from git) → derived → asserted (by an agent) → confirmed (by a human, via intent-confirm). Agents see which whys a human has actually vouched for.
• Capture loop. Agents call record_why when they make a structural choice and check_precedent before they make one. A pre-commit gate (install-hooks) warns — or blocks, with gate_hard — on structural changes that have no recorded why.
• Session bootstrap. bootstrap(task) returns top-level orientation plus the relevant whys within a token budget, with a degradation ladder: intent graph → code graph → raw files. It never hard-fails.
• Anchor honesty. intent-check re-anchors whys when code moves, flags whys whose code diverged, and reports conflicts and coverage.
• Human projection. intent-render produces an HTML or Mermaid view of the same graph for review.
• v1 migration. intent-migrate imports existing decision records. It's safe to re-run.
• Eval harness. intent-eval measures token cost and retrieval correctness against the v1 baseline. First self-hosted result: accuracy@1 100%, ~99% fewer tokens than a naive file read — on n=3 cases from this repo only. See docs/EVAL-RESULTS.md for methodology and caveats; external-repo numbers are still to come.

pip install -U codebase-intel
codebase-intel intent-migrate      # bring v1 decisions along
codebase-intel install-hooks       # start capturing whys at commit time

An agent skill that tells Claude Code (and other agents) when to call these tools ships in skills/codebase-intel/SKILL.md. Install it for Claude Code with:

mkdir -p ~/.claude/skills/codebase-intel
curl -fsSL https://raw.githubusercontent.com/a-mutharasu/codebase-intel/main/skills/codebase-intel/SKILL.md \
  -o ~/.claude/skills/codebase-intel/SKILL.md

New in v0.2.0

Global Workspace — One server, all your projects

No more running a separate MCP server per project. Register your repos once, serve them all:

codebase-intel register ~/projects/user-service
codebase-intel register /opt/services/payment-api
codebase-intel serve --auto

The server auto-routes each request to the correct project based on file paths. LRU cache keeps the 5 most recently used projects loaded — older ones are evicted and reloaded on demand.

Intent Tracking — "Did you actually build what was requested?"

AI agents say "done" when the code compiles. But did they actually deliver what was asked? Intent tracking captures goals with machine-verifiable acceptance criteria:

# Agent sets intent at task start (via MCP tool set_intent)
# Agent works on the task...
# Before marking done, agent calls check_intent
# System runs automated checks: file_exists, function_exists, grep_match, test_passes...
# Returns: 18/21 criteria met — 3 gaps identified

11 verification types: file_exists, file_contains, function_exists, wired, cli_works, mcp_tool_exists, grep_match, grep_no_match, test_passes, custom, manual.

Cross-Repo Awareness — Microservice dependency mapping

Scans 14 web frameworks across 10 languages to find exposed endpoints and outbound HTTP calls. Maps which service depends on which endpoint:

codebase-intel crossrepo --all --impact user-service

# Output:
# CRITICAL: 3 services depend on /api/v1/users/{id}
# → payment-service calls this endpoint [CRITICAL] at src/clients/user.py:42
# → notification-service calls this endpoint at lib/api/users.ts:18

Supported: FastAPI, Express, Flask, Django, Spring Boot, Gin, Actix, Rails, Phoenix, Laravel, ASP.NET, Ktor, Vapor, Echo.

Feedback Loop — Learn from acceptance/rejection

Records whether AI-generated code was accepted, modified, or rejected. Over time, identifies which context patterns lead to better output and which rejection reasons are most common.

Architecture

AI Agent (any) ──→ MCP Server (16 tools)
                        │
                  Workspace Manager ←── Global Registry (~/.codebase-intel/)
                  (multi-project routing, LRU cache)
                        │
                  Context Orchestrator
                  (token budgeting, priority, conflicts)
                   ╱          │          ╲
          Code Graph    Decision     Quality
          (19 langs)    Journal      Contracts
          SQLite+WAL    YAML files   YAML+builtins
                   ╲          │          ╱
                    Drift Detector
                    (staleness, rot, orphans)
                          │
               ┌──────────┼──────────┐
         Analytics    Feedback    Intent
         Tracker      Loop       Tracker
               └──────────┼──────────┘
                          │
                   Cross-Repo Scanner
                   (14 frameworks, 10 languages)

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The Philosophy

We don't make AI agents smarter. We make them informed.

An agent with 1M tokens of context is like a developer with access to every file in the company — overwhelming and unfocused. An agent with codebase-intel is like a developer who just had a 5-minute conversation with the senior engineer: "Here's what you need to know, here's why we did it this way, and here are the three things you absolutely cannot break."

We don't compete with graph tools. We complete them.

Code graphs answer "what depends on what." That's necessary but not sufficient. codebase-intel answers the harder questions: Why was this decision made? What constraints apply? What will the compliance team flag? What did we already try and reject?

We don't hide the truth. We prove it.

Run codebase-intel benchmark on your project. See the numbers. Run codebase-intel dashboard over time. Watch the improvement. Every claim is backed by reproducible, project-specific data.

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Contributing

Areas with the most impact:

1. Contract packs — Share quality rules for your framework
2. Language extraction — Improve parsing for specific languages
3. Decision mining — Better git history analysis
4. Benchmarks — Run against your repos, share results

git clone https://github.com/a-mutharasu/codebase-intel.git
cd codebase-intel
pip install -e ".[dev]"
pytest

Contact

Questions, partnerships or security reports: mutharasu.theofficial@gmail.com. For bugs and feature requests, please open an issue.

License

MIT