codeindex MCP server

codeindex

Temporal code knowledge graph with blast-radius impact scoring, semantic symbol search, and git-history-aware dependency analysis — for AI-assisted development.

Point it at any project — Python, JavaScript/TypeScript, Go, Ruby, Rust, Java, PHP, and more — and get:

• A persistent SQLite graph store at <repo>/.codeindex/index.db — incremental, queryable, temporal
• A codeindex.json dependency index written directly into your repo (preserved for backward compatibility)
• Per-file blast-radius scores (how many files break if this one changes), including historical as-of queries
• A symbolindex.json symbol map so AI can find any function/class without scanning every file
• Hybrid semantic search over symbols: natural-language queries fused with keyword + graph expansion
• Git history backfill — temporal graph from commit history without touching the working tree
• Ten ways to consume the data: CLI, markdown report, MCP server (10 tools), pre-commit hook, CLAUDE.md injection
• An interactive visualization UI (2D/3D graphs, dependency matrix, treemap)

No build step. No npm. Zero required runtime dependencies — SQLite is stdlib.

---

Install

pip install codeindex

Or from source:

git clone https://github.com/scheidydude/codeindex
cd codeindex
pip install -e .

---

Quickstart

# Build the dependency index (also writes to .codeindex/index.db)
codeindex analyze ./myapp

# Build the symbol index (where every function and class lives)
codeindex symbols ./myapp

# See blast radius for a file before touching it
codeindex impact src/auth.py

# Search symbols with natural language (no embedding endpoint needed — FTS fallback)
codeindex search "validate auth token"

# See what changed since a release tag
codeindex changed-since v1.2.0

# Launch the visualization UI
codeindex serve --viz --repo ./myapp
open http://localhost:8080

---

Commands

codeindex analyze

codeindex analyze [REPO_PATH] [--output PATH] [--watch]

Analyzes the repo and writes codeindex.json to the repo root. Detects 12+ languages automatically.

Flag	Default	Description
REPO_PATH	.	Path to repo root
--output	<repo>/codeindex.json	Override output path
--watch	off	Re-index on file changes (requires watchdog)

---

codeindex symbols

codeindex symbols [REPO_PATH] [--output PATH] [--inline] [--index PATH]
                  [--claude-md] [--claude-md-path PATH] [--all-symbols]

Builds a symbol index — a map of every function, class, struct, and type to its exact file and line number. Lets AI tools (and humans) find any symbol in one lookup instead of scanning the entire repo.

Modes:

Flag	Description
(none)	Write a standalone symbolindex.json
--inline	Embed symbols into each node in codeindex.json instead
--claude-md	Append a compressed symbol summary to CLAUDE.md

Both --inline and --claude-md can be combined in a single run.

Options:

Flag	Default	Description
REPO_PATH	.	Path to repo root
--output	<repo>/symbolindex.json	Output path (standalone mode)
--index	auto-discovered	Path to codeindex.json (for --inline)
--claude-md-path	<repo>/CLAUDE.md	Override CLAUDE.md path
--all-symbols	off	Include non-exported symbols in CLAUDE.md (default: exported only)

Examples:

# Standalone symbol index
codeindex symbols ./myapp

# Embed into codeindex.json (one file for blast radius + symbols)
codeindex symbols ./myapp --inline

# Write CLAUDE.md summary so Claude Code loads symbols automatically
codeindex symbols ./myapp --claude-md

# All three at once
codeindex symbols ./myapp --inline --claude-md

# Re-generate when code changes
codeindex symbols ./myapp --inline --claude-md

Why it matters: Claude Code and other AI tools normally scan every file to find a function definition. With a symbol index, Claude can load one file, do an O(1) lookup, and open only the relevant file — cutting token usage 60–90% on symbol-location tasks.

CLAUDE.md injection is opt-in because it increases base context size on every prompt. Use it when symbol lookups are frequent in your workflow; skip it for simple tasks where the overhead outweighs the benefit.

---

codeindex impact

codeindex impact FILE [--index PATH] [--out FILE] [--json] [--as-of REF]

Shows the blast-radius impact for a specific file: direct dependents, transitive dependents, blast score, and risk level.

Impact: src/auth.py
Blast Score: 8.5  (2 direct · 7 transitive)  [HIGH]

Direct dependents (2)
  src/api.py
  src/middleware.py

Transitive dependents (5 additional)
  src/main.py  ← src/api.py
  src/app.py   ← src/middleware.py
  ...

Risk: HIGH — affects 7/42 files (16.7% of codebase)

Blast score formula: direct + (0.5 × transitive)

Flag	Description
--index PATH	Path to codeindex.json (auto-discovered if omitted)
--out FILE	Write a markdown report to this file
--json	Output raw JSON
--as-of REF	Compute blast radius at a historical commit/ref instead of HEAD

---

codeindex search

codeindex search QUERY [--k N] [--as-of REF] [--db PATH] [--json]

Hybrid semantic + keyword + graph symbol search. Finds relevant functions and classes without knowing their exact names.

Retrieval signals fused with Reciprocal Rank Fusion (RRF):

1. Semantic KNN — embedding similarity (requires codeindex[semantic] + a configured endpoint)
2. FTS5 keyword — full-text search over symbol names, signatures, and docstrings
3. Graph expansion — structurally adjacent symbols from dependent/dependency files

Degrades gracefully: if no embedding endpoint is configured, falls back to FTS + graph (no crash, no config needed).

# Keyword + graph search (no embedding setup required)
codeindex search "validate auth token"

# Full semantic search (requires CODEINDEX_EMBEDDING_* env vars)
CODEINDEX_EMBEDDING_ENDPOINT=http://localhost:11434 \
CODEINDEX_EMBEDDING_MODEL=nomic-embed-text \
CODEINDEX_EMBEDDING_DIMS=768 \
codeindex search "validate auth token"

# Historical search — symbols visible at a release tag
codeindex search "token validation" --as-of v1.2.0

Flag	Default	Description
QUERY	—	Natural-language or keyword query
--k N	10	Number of results to return
--as-of REF	HEAD	Restrict to symbols visible at this commit/ref
--db PATH	auto-discovered	Path to .codeindex/index.db
--json	off	Output raw JSON

---

codeindex history

codeindex history [REPO_PATH] [--since REF] [--max-commits N] [--json]

Backfills temporal graph data from git history — without any working-tree checkouts. Reads blobs via git cat-file --batch and stamps first_seen_commit / last_seen_commit on every file, edge, and symbol.

Run this once after initial setup to enable --as-of queries across the full history.

# Backfill up to 1000 commits (default)
codeindex history .

# Backfill only recent history
codeindex history . --since v1.0.0 --max-commits 200

Flag	Default	Description
REPO_PATH	.	Path to repo root
--since REF	—	Only process commits after this date/ref
--max-commits N	1000	Maximum commits to process
--json	off	Output summary as JSON

---

codeindex changed-since

codeindex changed-since REF [--repo PATH] [--db PATH] [--json]

Lists files and dependency edges added or removed since a commit, branch, or tag.

$ codeindex changed-since v1.2.0
Changes since v1.2.0:

  Added files (2):
    + src/payments/stripe.py
    + src/payments/webhook.py

  Removed edges (1):
    - src/api.py → src/auth_v1.py  [imports]

Flag	Default	Description
REF	—	Commit hash, branch, or tag to compare against
--repo PATH	.	Repo root (for git operations)
--db PATH	auto-discovered	Path to .codeindex/index.db
--json	off	Output raw JSON

---

codeindex db

codeindex db status [--db PATH] [--json]
codeindex db migrate [--db PATH]

Manages the SQLite store at <repo>/.codeindex/index.db.

$ codeindex db status
schema_version      : 2
repo_root           : /Users/alice/myapp
last_indexed_commit : a3f2e1c8
active_files        : 142
active_edges        : 387
active_symbols      : 1204
embedding_model     : nomic-embed-text
embedding_dims      : 768
vec_symbols         : enabled

db migrate applies any pending schema migrations automatically (also runs on every codeindex analyze).

---

codeindex serve

codeindex serve --viz [--repo PATH] [--port PORT] [--watch]
codeindex serve --mcp

--viz launches an interactive visualization UI in your browser (5 modes: 2D force graph, 3D network, dependency matrix, treemap, infrastructure graph).

--mcp starts a stdio MCP server that exposes codeindex tools directly to Claude and other MCP clients.

MCP tools:

Tool	Description
analyze_repo	Build or refresh the dependency index
get_impact	Blast-radius report for a file
get_dependencies	imports + imported-by for a file
get_high_blast_files	All files above a blast score threshold
build_symbol_index	Build or refresh the symbol index
lookup_symbol	Find where any function/class/type is defined (file + line)
semantic_search	Hybrid semantic + keyword + graph symbol search; degrades gracefully without embeddings
temporal_impact	Blast-radius at a historical commit/ref (as_of parameter)
graph_query	k-hop dependency neighborhood of a file (dependents/dependencies/both)
changed_since	Files and edges added or removed since a commit/ref

Claude Code MCP config (.claude/settings.json):

{
  "mcpServers": {
    "codeindex": {
      "command": "codeindex",
      "args": ["serve", "--mcp"]
    }
  }
}

---

codeindex lookup

codeindex lookup SYMBOL [--index PATH] [--json]

Finds where a function, class, struct, or other symbol is defined. Queries the SQLite DB (same source as search), falling back to symbolindex.json if no DB is present. Prints 5 lines of source context around the definition.

$ codeindex lookup compute_blast_radius
codeindex/impact.py:6  compute_blast_radius  (function)

  >    6 | def compute_blast_radius(nodes: list[dict], links: list[dict]) -> dict[str, dict]:
         7 |     """..."""
         8 |     ...

$ codeindex lookup AuthService
src/auth.py:44  AuthService  (class)  methods: login, logout, refresh

  >   44 | class AuthService:
        45 |     def login(self, ...):

If a symbol isn't found, it's likely a third-party import — only symbols defined in the repo are indexed.

Flag	Description
--index PATH	Path to symbolindex.json fallback (auto-discovered if omitted)
--json	Output raw JSON

---

codeindex dependencies

codeindex dependencies FILE [--index PATH] [--json]

Shows what a file imports and what imports it, plus its blast score.

$ codeindex dependencies src/auth.py
File: src/auth.py  (blast score: 8.5)

Imports (3):
  src/db.py
  src/config.py
  src/utils.py

Imported by (2):
  src/api.py
  src/middleware.py

Flag	Description
--index PATH	Path to codeindex.json (auto-discovered if omitted)
--json	Output raw JSON

---

codeindex high-blast

codeindex high-blast [--threshold N] [--index PATH] [--json]

Lists all files whose blast score exceeds the threshold, sorted by score descending. Useful for identifying the riskiest files before a refactor.

$ codeindex high-blast --threshold 5
Files with blast score ≥ 5.0  (3 found)

  13.0  src/db.py          (12d / 2t)
   8.5  src/auth.py        (3d / 7t)
   5.5  src/config.py      (5d / 1t)

d = direct dependents · t = transitive dependents

Flag	Default	Description
--threshold N	5	Minimum blast score to include
--index PATH	auto-discovered	Path to codeindex.json
--json	off	Output raw JSON

---

codeindex symbol-blast

codeindex symbol-blast FILE [--json]

Per-export blast radius for a file. Lists every exported symbol with the count and exact file paths of importers that reference it by name. Useful when a file exports many symbols and you only need to touch one — lets you confirm the others are safe.

$ codeindex symbol-blast lib/db/schema.ts

Symbol-level blast radius: lib/db/schema.ts

  5 exported symbol(s), 12 importer(s)

  userSchema  (const, line 8)  →  8 user(s)
    app/api/users/route.ts
    app/api/profile/route.ts
    ...
  legacySchema  (const, line 42)  →  1 user(s)
    scripts/migrate.ts
  sessionSchema  (const, line 67)  →  3 user(s)
    ...

userSchema touches 8 routes; legacySchema touches only 1 — safe to change in isolation.

Flag	Description
FILE	Repo-relative path to the file (e.g. lib/db/schema.ts)
--json	Output raw JSON with full used_by arrays per symbol

---

codeindex install-hook

codeindex install-hook [--repo PATH] [--threshold N] [--strict] [--remove]

Installs a git pre-commit hook that warns when staged files exceed the blast score threshold.

Flag	Default	Description
--threshold N	10	Blast score above which to warn
--strict	off	Block the commit instead of just warning
--remove	—	Uninstall the hook

---

Using codeindex in another repo with Claude

Three workflows, ordered by automation level.

Workflow 1 — MCP server (recommended for active coding)

Claude gets symbol lookup, dependency, and impact tools it calls automatically. No extra prompting needed.

One-time setup:

cd /your/other/repo
codeindex analyze .
codeindex symbols .

Register the MCP server with Claude Code using claude mcp add. Use --scope project to limit it to this repo, or --scope global to use it everywhere:

# Project-scoped (recommended — stored in .claude/settings.json)
claude mcp add --scope project codeindex -- /path/to/codeindex serve --mcp

# Global (available in all repos)
claude mcp add --scope global codeindex -- /path/to/codeindex serve --mcp

Find the full path to your codeindex binary with which codeindex, then substitute it above.

# Example with conda install
claude mcp add --scope project codeindex -- /opt/homebrew/Caskroom/miniforge/base/bin/codeindex serve --mcp

Verify it registered:

claude mcp list

Note: Do not use "command": "codeindex" with a bare name — Claude Code does not inherit your shell PATH, so the binary won't be found unless you use the absolute path.

Claude now has all 10 MCP tools available in every session. When it needs to find processPayment, it calls lookup_symbol("processPayment") and gets src/billing.py:142 back in one shot — no file scanning. When it needs to find code that validates auth tokens without knowing the exact name, it calls semantic_search("validate auth token").

Keep the index fresh:

# Auto-rebuild on file changes (leave running in a terminal)
codeindex symbols . --watch

---

Workflow 2 — CLAUDE.md injection (best for repos you revisit often)

Symbol table is embedded in CLAUDE.md so it loads into every session automatically — no tool call needed at all.

cd /your/other/repo
codeindex symbols . --claude-md

This upserts a symbolindex code fence into CLAUDE.md. Every Claude Code session in that repo loads it at startup. Claude can answer "where is X defined?" from context alone with zero tool calls.

Tradeoff: adds ~500–2000 tokens to every prompt depending on repo size. Worth it for repos where symbol lookups are frequent; skip it for repos where you mostly write new code.

Keep it fresh:

# Re-run after significant refactors
codeindex analyze . && codeindex symbols . --claude-md

---

Workflow 3 — Hybrid (large repos)

For large repos where the --claude-md section would be too large, use the MCP server for lookups and add a short hint to CLAUDE.md so Claude reaches for the tool first:

codeindex analyze .
codeindex symbols .

Then add to CLAUDE.md:

## Codeindex
Symbol index: `symbolindex.json` — use the `lookup_symbol` MCP tool before grepping for any function or class.
Dependency index: `codeindex.json` — use `get_impact` before modifying high-blast files.

This costs almost no tokens but primes Claude to use the index rather than defaulting to grep.

---

CLI quick reference for human use

The same data available via MCP is also accessible directly from the terminal:

# Find where a symbol is defined (shows code snippet)
codeindex lookup MyClassName
codeindex lookup process_payment --json

# Show what a file imports and what depends on it
codeindex dependencies src/auth.py

# List the riskiest files to change
codeindex high-blast --threshold 5

# Blast-radius report before touching a file
codeindex impact src/auth.py

# Per-export blast radius — which importers use each exported symbol
codeindex symbol-blast lib/db/schema.ts

---

Which workflow to pick

Situation	Workflow
Daily driver repo, active feature work	MCP server
Medium repo, frequent symbol lookups	CLAUDE.md injection
Large repo (1000+ files)	MCP server + short CLAUDE.md hint
Quick one-off in an unfamiliar repo	codeindex symbols . --claude-md, delete after
Terminal / scripting use	CLI commands (lookup, dependencies, high-blast)

---

Supported Languages

Language	Dependency analysis	Symbol extraction
Python	AST imports, type detection	Functions, classes, methods (AST-precise)
JavaScript / TypeScript	ES modules, require(), framework detection	Exported functions, classes, types, enums, consts
Vue	SFC <script> imports	Exported symbols from <script> block
Go	Package-level nodes, import blocks	Functions, structs, interfaces (exported flag)
Ruby	require, require_relative, autoload	Classes, modules, methods
Rust	mod, use crate::	pub fn, structs, enums, traits
Java / Kotlin	FQN imports, wildcard imports	Classes, interfaces, methods
PHP	PSR-4 namespace resolution	Classes, interfaces, functions
CSS / SCSS / Less	@import, @use, @forward	—
Docker	Services, depends_on edges	—
CI/CD	GitHub Actions + GitLab CI jobs, needs: edges	—
SQL / Prisma	Tables/models, foreign key edges	—

---

Output schemas

codeindex.json

{
  "meta": {
    "root": "myapp/",
    "total_files": 60,
    "total_loc": 4085,
    "languages": ["python", "javascript"]
  },
  "nodes": [
    {
      "id": "src/auth.py",
      "type": "module",
      "language": "python",
      "layer": "backend",
      "loc": 142,
      "imports": ["src/db.py"],
      "imported_by": ["src/api.py", "src/middleware.py"],
      "direct_dependents": 2,
      "transitive_dependents": 7,
      "blast_score": 5.5,
      "symbols": [
        { "name": "verify_token", "line": 18, "kind": "function", "exported": true },
        { "name": "AuthService",  "line": 44, "kind": "class",    "exported": true,
          "methods": ["login", "logout", "refresh"] }
      ]
    }
  ],
  "links": [
    { "source": "src/api.py", "target": "src/auth.py", "weight": 1, "kind": "imports" }
  ]
}

The symbols field is only present when codeindex symbols --inline has been run.

---

symbolindex.json

{
  "meta": {
    "generated": "2026-05-21",
    "repo": "myapp/",
    "total_symbols": 312
  },
  "symbols": {
    "verify_token": [
      {
        "file": "src/auth.py",
        "line": 18,
        "kind": "function",
        "exported": true,
        "doc": "Verify a JWT and return the decoded payload."
      }
    ],
    "AuthService": [
      {
        "file": "src/auth.py",
        "line": 44,
        "kind": "class",
        "exported": true,
        "methods": ["login", "logout", "refresh"]
      }
    ]
  },
  "file_symbols": {
    "src/auth.py": [
      { "name": "verify_token", "line": 18, "kind": "function", "exported": true },
      { "name": "AuthService",  "line": 44, "kind": "class",    "exported": true,
        "methods": ["login", "logout", "refresh"] }
    ]
  }
}

Lookup patterns:

• "Where is verify_token defined?" → symbols["verify_token"][0].file + .line — O(1)
• "What symbols live in src/auth.py?" → file_symbols["src/auth.py"] — O(1)
• "What's the blast radius of changing verify_token?" → cross-reference codeindex.json via the file

---

CLAUDE.md symbol section

When --claude-md is used, a compact section is upserted into CLAUDE.md bounded by HTML comment markers so re-runs update in place:

<!-- codeindex-symbols-start -->
## Symbol Index
_Generated by codeindex. Update: `codeindex symbols --claude-md`_

```symbolindex
src/auth.py: verify_token:fn:18 AuthService:cls:44[login,logout,refresh]
src/db.py: connect:fn:12 query:fn:28 close:fn:55

Format per symbol: `name:kind_abbr:line[methods...]`
Kind abbreviations: `fn` function · `cls` class · `st` struct · `en` enum · `tr` trait · `if` interface · `ty` type · `co` const

---

## AI workflow comparison

| Task | Without codeindex | With symbolindex.json |
|------|-------------------|----------------------|
| Find where `process_payment` is defined | Grep / scan ~200 files | Load 1 file, O(1) lookup |
| Understand blast radius of a change | Manual tracing | `codeindex impact <file>` |
| Load only relevant context | Full repo scan | File + line from symbol map |
| Estimated token savings | baseline | **60–90% on symbol tasks** |

---

## Optional dependencies

| Package | Purpose | Install |
|---------|---------|---------|
| `sqlite-vec` | Semantic vector search in `codeindex search` and `semantic_search` MCP tool | `pip install 'codeindex[semantic]'` |
| `watchdog` | `--watch` file change detection | `pip install 'codeindex[watch]'` |
| `PyYAML` | Better Docker Compose / CI YAML parsing | `pip install 'codeindex[yaml]'` |
| `tomli` | Rust `Cargo.toml` on Python < 3.11 | `pip install 'codeindex[toml]'` |

### Semantic search configuration

Semantic search requires a self-hosted embedding endpoint (Ollama, LM Studio, llama.cpp server, or any OpenAI-compatible `/v1/embeddings` API) and the `sqlite-vec` extension.

```bash
pip install 'codeindex[semantic]'

# Set env vars (add to your shell profile or .env)
export CODEINDEX_EMBEDDING_ENDPOINT=http://localhost:11434
export CODEINDEX_EMBEDDING_MODEL=nomic-embed-text
export CODEINDEX_EMBEDDING_DIMS=768

# Re-index to generate embeddings
codeindex analyze ./myapp

# Search
codeindex search "validate JWT token"

Without these env vars, codeindex search and the semantic_search MCP tool fall back to FTS5 keyword + graph search — no crash, no config required.

---

Requirements

• Python 3.9+
• A modern browser (for --viz mode)

---

License

Apache 2.0 — free to use and build on; attribution required in derivative works and documentation. Copyright 2026 David Scheiderman.