Cognirepo MCP Server

CogniRepo

mcp-name: io.github.ashlesh-t/cognirepo

Persistent memory and context for any AI tool. Not a chatbot — infrastructure.

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lookup_symbol returns file:line very quickly — grep takes 2–8 seconds. On Python repos ≥ 15K LOC, CogniRepo cuts AI coding agent token usage by 50–80% compared to raw file reads — benchmarked on Flask, FastAPI, Celery, and Ansible (1,800+ files). Works with Claude Code, Cursor, and Gemini CLI. Fully offline. No API keys required for indexing or any of the 34 MCP tools.

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What it does

Every AI conversation starts from zero. Claude, Cursor, Gemini — none of them remember what you fixed yesterday, which files relate to which features, or what decisions were made last sprint. CogniRepo fixes that.

It sits between your codebase and any AI tool, providing:

• Semantic memory — FAISS vector store with sentence-transformer embeddings. Store decisions, docs, architecture notes. Retrieve them with natural language.
• Episodic log — append-only event journal. Know what happened before that error.
• Knowledge graph — NetworkX DiGraph linking functions, classes, files, imports, inheritance chains, call relationships, and concepts. All queryable.
• AST reverse index — O(1) symbol lookup across your entire codebase in any supported language.
• User behavior profiling — tracks how you prompt so Claude adapts its response style without you having to re-explain preferences every session.
• Error tracking — records errors with prevention hints so Claude avoids repeating the same mistake across sessions.
• Session history — persists conversation exchanges so any session can resume where the last one ended.
• Architectural summaries — auto-generated on first init; built entirely from the local AST index (no API key needed). File → directory → repo summary tree, embedded into FAISS for semantic search.
• Multi-model orchestration — classify query complexity → build context → route to the right model. Claude for deep reasoning, Gemini Flash for quick lookups. All automatic.

Every AI tool that connects gets the same accumulated project knowledge. Memory persists across sessions, across tools, across time.

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When to use CogniRepo

Most effective on codebases ≥ 15K LOC. On small repos (< 10K LOC), native file reads are fast enough that the MCP tool schema overhead (~4,100 tokens for 34 tools) takes more than you save. Break-even is roughly 4 tool calls on a medium-sized repo.

CogniRepo vs. claude-context / similar tools:

Conclusion: prefer CogniRepo when you value institutional memory across sessions. Use simpler tools when you just need one-shot code retrieval on a small codebase.

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Why it helps — measured numbers

Benchmarked across 6 real open-source repos (FastAPI, Flask, Celery, Ansible, Moby/Docker, Kubernetes) using 30 structured prompts tested against Claude, Gemini, and Cursor/Codex.

Honest limits: CogniRepo adds the most value on Python repos with clear static structure. Dynamic dispatch patterns (Celery beat, plugin registries), deep Go codebases, and Ansible's 22-level variable precedence chains reduce retrieval confidence. The tool reports uncertainty rather than hallucinating call chains.

Measured: precision@k and index build time (4 external repos)

Indexed 4 real repos, measured with cognirepo index-repo + context_pack queries. CPU-only, no GPU.

All repos: symbol hit rate 5/5, lookup latency < 0.1ms. All quality gates pass. Full numbers: docs/METRICS.md.

Run cognirepo benchmark on your own codebase to reproduce. See docs/METRICS.md.

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How it works

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Quick start

Requirements

• Python 3.11+
• API key (optional — only needed for cognirepo ask): ANTHROPIC_API_KEY, GEMINI_API_KEY, OPENAI_API_KEY, or GROK_API_KEY. Indexing, memory, summarization, and all MCP tools work fully offline.

Install

Recommended — pipx (global, one command, works on all distros)

pipx install cognirepo

That's it. cognirepo setup handles the rest — it installs optional extras (languages, security, providers) via pipx inject automatically when you enable them in the wizard.

Why pipx? It creates an isolated venv for cognirepo automatically so fastembed and all deps install cleanly. The cognirepo command is then globally available in every directory — no per-repo venv needed.

Arch Linux / Debian 12+ / Ubuntu 24.04+: Do NOT pip install into system Python. These distros enforce PEP 668 and block system-wide pip installs. Use pipx.

Install pipx first (if needed)

# Arch Linux
sudo pacman -S python-pipx

# Debian / Ubuntu
sudo apt install pipx

# macOS
brew install pipx

# Any platform (fallback)
pip install pipx --user

Inside a virtual environment (alternative)

python -m venv .venv && source .venv/bin/activate
pip install cognirepo
# extras are installed by the setup wizard automatically

Development install (from source)

pipx install -e '.[dev,security,languages]'
# or inside a venv: pip install -e '.[dev,security,languages]'

Note: CPU-only embeddings are the default (fastembed/ONNX, no PyTorch/CUDA required). For GPU: pipx inject cognirepo 'cognirepo[gpu]' then install torch separately.

Run

# One-command onboarding (init + index + auto-configure MCP for Claude/Cursor/VS Code):
cognirepo setup

# Or step by step:
cognirepo init --no-index     # scaffold .cognirepo/
cognirepo index-repo .        # index your codebase (required before MCP tools work)
cognirepo index-repo . --daemon  # index and run watcher in background

# Check everything is working:
cognirepo status                        # shows symbol count, graph nodes, signal warmth
cognirepo doctor                        # full health check

# Query through multi-model orchestrator:
cognirepo ask "why is auth slow?"

# Manage background watchers:
cognirepo list                          # show all running watcher daemons
cognirepo list -n <PID> --view          # tail the log of a specific watcher
cognirepo list -n <PID> --stop          # stop a watcher

First-time setup: cognirepo init + cognirepo index-repo . must complete before MCP tools (context_pack, lookup_symbol, who_calls, etc.) return data.

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Connect your AI tools

Claude Code / Claude Desktop (recommended — project-scoped)

Run cognirepo init inside your project — it asks if you want to configure Claude and automatically writes .claude/CLAUDE.md and .claude/settings.json with the correct project-locked connector.

Each project gets its own isolated connector named cognirepo-<project>:

{
  "mcpServers": {
    "cognirepo-myproject": {
      "command": "cognirepo",
      "args": ["serve", "--project-dir", "/abs/path/to/myproject"],
      "env": {}
    }
  }
}

The --project-dir flag locks the MCP server to that project's .cognirepo/ directory. When Claude has multiple projects open simultaneously, each connector reads only its own memories — never mixing data across projects or teams.

Cursor / Copilot

cognirepo export-spec
cp adapters/cursor_mcp_config.json .cursor/mcp.json
# Restart Cursor — CogniRepo tools appear in the tool selector

Docker

cp .env.example .env          # add your API keys
docker compose up mcp         # MCP stdio server

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MCP Tools — complete reference

All 34 tools are available to Claude, Cursor, and any MCP-compatible client.

Core retrieval

User & session intelligence

Error tracking & prevention

Session start

Memory & storage

Cross-repo (organization)

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Knowledge graph — what gets indexed

The knowledge graph is significantly richer than a simple call graph.

Node types

Edge types

IMPORTS and INHERITS edges are built automatically during index-repo from Python AST. Use subgraph("MyClass", depth=2) or dependency_graph("mymodule") to query them.

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User behavior profiling

CogniRepo tracks how you interact across sessions and builds a profile that Claude uses to calibrate its responses — without you having to repeat preferences every session.

What gets tracked

• Depth preference — inferred from average query length: concise / medium / detailed
• Question types — distribution across: why, what, how, fix, explain, where, refactor, add
• Domain vocabulary — top terms that appear frequently in your queries
• Code focus — percentage of queries referencing code identifiers (symbols, functions)
• Sample queries — last 3 queries for Claude to infer framing style

Accessing your profile

# MCP tool (Claude calls automatically at session start):
get_user_profile()

# CLI:
cognirepo user-prefs

Example profile output

{
  "depth_preference": "detailed",
  "top_question_type": "how",
  "question_type_distribution": {"how": 12, "why": 8, "fix": 5},
  "top_terminology": ["auth", "token", "session", "middleware", "validate"],
  "code_focus_percent": 73,
  "framing_hints": "prefers detailed responses; often asks 'how' questions; domain vocabulary: auth, token, session",
  "total_queries_tracked": 47
}

Claude receives framing_hints at session start and adjusts response length, code density, and terminology accordingly. The profile accumulates over time — more accurate the more you use it.

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Error tracking & prevention

CogniRepo logs every error that occurs during sessions — whether it's a Python exception, a failed build step, or a tool call that went wrong. Errors are stored with:

• Dedup signature — prevents the same error from inflating the count
• Prevention hint — a targeted suggestion to avoid the same error class
• Occurrence context — last 5 occurrences with file path and error message
• Query context — the query or action that triggered the error

Logging errors

# MCP tool (Claude calls after errors):
record_error("TypeError", "expected str got int", "config/parser.py", "fix config loading")

Viewing error patterns

# MCP tool:
get_error_patterns()

Returns:

[
  {
    "error_type": "TypeError",
    "count": 7,
    "files": ["config/parser.py", "api/handlers.py"],
    "last_seen": "2026-04-22T10:30:00Z",
    "prevention_hint": "Wrong type — validate inputs at function boundary.",
    "recent_context": "expected str got int in parse_config"
  }
]

Built-in prevention hints

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Session history

Every cognirepo ask exchange is persisted to .cognirepo/sessions/. Sessions are indexed by UUID and retrievable via:

# List recent sessions:
cognirepo sessions

# MCP tool — Claude calls at session start to resume context:
get_session_history(limit=5)

Each entry returns: session ID, created timestamp, message count, model used, and the last user/assistant exchange for quick context scan.

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Architectural summaries

cognirepo init automatically prompts to run cognirepo summarize after the first index. This produces a 3-level LLM summary of the entire codebase:

• Level 1 — repo-wide summary (what the project does, key modules, entry points)
• Level 2 — per-directory summaries (what each package is responsible for)
• Level 3 — per-file summaries (what each file contains, key functions/classes)

Summaries are stored in .cognirepo/index/summaries.json and served via the architecture_overview MCP tool — zero token cost for Claude to understand the big picture.

# Auto-prompted on first init. Run manually anytime:
cognirepo summarize

# Fully local — no API key required. Reads from ast_index.json, runs in < 1 second.
# File summaries are also embedded into FAISS for semantic architecture queries.

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Multi-model orchestration

cognirepo ask automatically picks the right model for each query:

cognirepo ask "where is verify_token defined?"       # → QUICK, answered locally
cognirepo ask "why is auth slow?"                    # → EXPERT, Claude with full context
cognirepo ask --verbose "explain the circuit breaker"  # show tier/score/signals

Provider fallback chain: Grok → Gemini → Anthropic → OpenAI. All errors are logged to .cognirepo/errors/<date>.log — no raw tracebacks shown to users.

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Language support

Full details and roadmap: docs/LANGUAGES.md

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Storage layout

.cognirepo/
  config.json              ← project settings (project_id, model, retrieval weights)
  vector_db/
    semantic.index         ← FAISS flat index for semantic memory
    ast.index              ← FAISS IndexIDMap2 for code symbols
    ast_metadata.json      ← parallel metadata for ast.index rows
  graph/
    graph.pkl              ← NetworkX DiGraph (optionally Fernet-encrypted)
    behaviour.json         ← per-symbol hit counts, user profile, error patterns
  index/
    ast_index.json         ← reverse symbol index + file records
    manifest.json          ← git SHA + platform info for integrity checks
    summaries.json         ← LLM architectural summaries (Level 1–3)
  memory/
    episodic.json          ← append-only event journal
  sessions/
    <uuid>.json            ← conversation session files
    current.json           ← pointer to most-recent session
  errors/
    <date>.log             ← daily error logs (full tracebacks, never shown to users)
  learnings/
    learnings.json         ← structured learnings: decisions, bugs, prod issues

Everything under .cognirepo/ is .gitignored by default — never committed. Fernet encryption is opt-in at storage.encrypt: true in config.json.

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CLI reference

# Setup
cognirepo init                  # scaffold + configure; auto-indexes + auto-summarizes
cognirepo setup-env             # interactive API key wizard
cognirepo test-connection       # test API key connectivity
cognirepo migrate-config        # migrate deprecated config keys

# Indexing
cognirepo index-repo [path]     # AST-index a codebase
cognirepo summarize             # generate LLM architectural summaries (auto-prompted on init)
cognirepo seed --from-git       # seed behaviour weights from git history
cognirepo verify-index          # verify AST index integrity
cognirepo coverage              # per-directory symbol counts

# Querying
cognirepo ask <query>           # route through multi-model orchestrator
cognirepo retrieve-memory <q>   # similarity search
cognirepo search-docs <q>       # full-text search in .md files
cognirepo log-episode <event>   # append episodic event
cognirepo history               # print recent episodic events
cognirepo sessions              # list recent conversation sessions

# Memory management
cognirepo store-memory <text>   # save a semantic memory
cognirepo user-prefs            # view/set global user preferences
cognirepo prune [--dry-run]     # prune low-score memories

# Health & monitoring
cognirepo prime                 # generate session bootstrap brief
cognirepo status                # live retrieval signal weights + index health
cognirepo doctor [--fix]        # full health check; --fix auto-repairs common issues
cognirepo benchmark             # run quantitative value benchmarks

# Organization
cognirepo org create <name>     # create local organization
cognirepo org link <org> [path] # link repo to organization
cognirepo org list              # list organizations

# Daemon management
cognirepo list                  # list MCP servers, running daemons
cognirepo watch                 # manage background file-watcher daemon

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Future Plans

Priorities drawn from the v0.3.0 benchmark findings and community feedback.

Near-term (v0.3.0)

• Go call-graph indexing — tree-sitter-go grammar is loaded but call extraction is incomplete; Moby/Kubernetes tests (MO-3-5, K8-*) could not be completed without it. Adding Go-aware who_calls and IMPORTS edges is the single highest-impact unblocked item.
• cognirepo ask — multi-model orchestrator (QUICK/STANDARD/COMPLEX/EXPERT tiers). Initial implementation stubbed in v0.2.0; orchestrator logic is implemented in orchestrator/ and being wired to a working API key flow in v0.3.0.
• Incremental re-index on save — file-watcher daemon exists (cognirepo watch) but re-index on write is not yet debounced correctly; large repos see spurious full re-indexes.
• CLAUDE.md mandatory-call relaxation — benchmark feedback (Moby tests) flagged that forcing context_pack before every file read adds latency under memory pressure. Will add a --fast mode that skips the tool-first gate for files under 50 lines.

Medium-term (v0.4.0)

• Kubernetes / 2M-LOC scale validation — K8-1 through K8-5 test suite not yet completed. Goal: full scheduling-decision trace at < 8 000 tokens with CogniRepo vs. > 50 000 without.
• Plugin-registry pattern detection — Ansible AN-3/AN-4 (22-level variable precedence, strategy plugins) and Celery CE-3 (dynamic dispatch) returned NA. Plan: static heuristic pass that detects register, entry_points, and __init_subclass__ patterns and annotates them as DYNAMIC_DISPATCH nodes in the graph.
• BM25 over symbol names — current keyword search uses exact-word reverse index; adding BM25 TF-IDF ranking over symbol names and docstrings would improve partial-match recall (e.g. HttpClient matching http_client).
• Cross-session memory warm-up — Ansible benchmark noted episodic/memory retrieval is low-value on fresh sessions. cognirepo prime exists but is not run automatically on init; will make it opt-in default.

Longer-term

• cognirepo ask streaming REPL — full interactive session with tier routing, session persistence, and sub-agent delegation.
• Ruby, PHP, C#, Swift grammar support — tree-sitter grammars exist; need _TS_FUNCTION_TYPES/_TS_CLASS_TYPES mappings and call-extraction rules per language.
• Similarity edges in knowledge graph — embedding-distance clustering to connect semantically related symbols across files (not yet implemented).
• VS Code / JetBrains extension — surface lookup_symbol, context_pack, and who_calls directly in the editor sidebar without requiring an MCP-capable host.

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Documentation

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License

CogniRepo is licensed under the MIT License.

• Free to use, study, modify, and distribute
• Use in proprietary products and commercial services — no restrictions
• No requirement to open-source your application

See LICENSE for full details.