GitNexus/gitnexus/README.md

GitNexus

Graph-powered code intelligence for AI agents. Index any codebase into a knowledge graph, then query it via MCP or CLI.

Works with Cursor, Claude Code, Antigravity (Google), Codex, Windsurf, Cline, OpenCode, CodeBuddy (Tencent), Qoder (Alibaba), and any MCP-compatible tool.

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Why?

AI coding tools don't understand your codebase structure. They edit a function without knowing 47 other functions depend on it. GitNexus fixes this by precomputing every dependency, call chain, and relationship into a queryable graph.

Three commands to give your AI agent full codebase awareness.

Quick Start

# Index your repo (run from repo root)
npx gitnexus analyze

That's it. This indexes the codebase, installs agent skills, registers Claude Code hooks, and creates AGENTS.md / CLAUDE.md context files — all in one command.

On npm 11.x? npx can crash during install (Cannot destructure property 'package' of 'node.target'). Use the pnpm form instead:

pnpm --allow-build=@ladybugdb/core --allow-build=gitnexus --allow-build=tree-sitter dlx gitnexus@latest analyze

See Troubleshooting → npx gitnexus crashes with node.target is null (npm 11) for the full matrix (global install, npm downgrade).

To configure MCP for your editor, run npx gitnexus setup once — or set it up manually below.

gitnexus setup auto-detects your editors and writes the correct global MCP config. You only need to run it once. To configure only selected integrations, pass --coding-agent/-c with a comma-separated list or repeat the option, for example gitnexus setup -c cursor,codex.

Editor Support

Editor	MCP	Skills	Hooks (auto-augment)	Support
Claude Code	Yes	Yes	Yes (PreToolUse + PostToolUse)	Full
Cursor	Yes	Yes	Yes (postToolUse, manual install)	Full
Antigravity (Google)	Yes	Yes	Yes (AfterTool, Gemini CLI hooks schema)	Full
Codex	Yes	Yes	Yes (PreToolUse + PostToolUse, Codex hooks)	Full
OpenCode	Yes	Yes	—	MCP + Skills
CodeBuddy (Tencent)	Yes	Yes	—	MCP + Skills
Qoder (Alibaba)	Yes	Yes	—	MCP + Skills
Windsurf	Yes	—	—	MCP

Claude Code and Codex get the deepest integration: MCP tools + agent skills + PreToolUse hooks that automatically enrich grep/glob/bash calls with knowledge graph context + PostToolUse hooks that detect a stale index after commits and prompt the agent to reindex.

Community Integrations

Agent	Install	Source
pi	pi install npm:pi-gitnexus	pi-gitnexus

MCP Setup (manual)

If you prefer to configure manually instead of using gitnexus setup:

Claude Code (full support — MCP + skills + hooks)

# macOS / Linux
claude mcp add gitnexus -- npx -y gitnexus@latest mcp

# Windows
claude mcp add gitnexus -- cmd /c npx -y gitnexus@latest mcp

Codex (full support — MCP + skills + hooks)

codex mcp add gitnexus -- npx -y gitnexus@latest mcp

Codex hooks (PreToolUse graph enrichment + PostToolUse stale-index detection in ~/.codex/hooks.json, same schema as Claude Code) need the bundled adapter script, so they are installed by gitnexus setup -c codex rather than manually.

Alternatively, install everything as a Codex plugin (MCP + skills + hooks in one step):

codex plugin marketplace add abhigyanpatwari/GitNexus
# then inside Codex: /plugins → install "GitNexus"

Codex notes: SessionStart is intentionally not registered — Codex reads AGENTS.md natively, which already carries the GitNexus context block. Newly installed hooks need a one-time approval in Codex via /hooks before they run. Pick one install route (gitnexus setup -c codex or the plugin): plugin hooks load alongside ~/.codex/hooks.json, so installing both can fire duplicate hooks per tool call.

Cursor / Windsurf

Add to ~/.cursor/mcp.json (global — works for all projects):

{
  "mcpServers": {
    "gitnexus": {
      "command": "npx",
      "args": ["-y", "gitnexus@latest", "mcp"]
    }
  }
}

OpenCode

Add to ~/.config/opencode/config.json:

{
  "mcp": {
    "gitnexus": {
      "command": "npx",
      "args": ["-y", "gitnexus@latest", "mcp"]
    }
  }
}

CodeBuddy

CodeBuddy reads only the first existing file in its config priority chain: ~/.codebuddy/.mcp.json (recommended) → ~/.codebuddy/mcp.json (deprecated) → ~/.codebuddy.json (legacy). Edit the first non-empty file that exists — creating a higher-priority file would hide the servers in the ones below it. If none exist, create ~/.codebuddy/.mcp.json:

{
  "mcpServers": {
    "gitnexus": {
      "command": "npx",
      "args": ["-y", "gitnexus@latest", "mcp"]
    }
  }
}

Qoder

Add to ~/.qoder.json:

{
  "mcpServers": {
    "gitnexus": {
      "command": "npx",
      "args": ["-y", "gitnexus@latest", "mcp"]
    }
  }
}

How It Works

GitNexus builds a complete knowledge graph of your codebase through a multi-phase indexing pipeline:

1. Structure — Walks the file tree and maps folder/file relationships
2. Parsing — Extracts functions, classes, methods, and interfaces using Tree-sitter ASTs
3. Resolution — Resolves imports and function calls across files with language-aware logic
   • Field & Property Type Resolution — Tracks field types across classes and interfaces for deep chain resolution (e.g., user.address.city.getName())
   • Return-Type-Aware Variable Binding — Infers variable types from function return types, enabling accurate call-result binding
4. Clustering — Groups related symbols into functional communities
5. Processes — Traces execution flows from entry points through call chains
6. Search — Builds hybrid search indexes for fast retrieval

The result is a LadybugDB graph database stored locally in .gitnexus/ with full-text search and semantic embeddings.

Experimental community detection engine

Community detection uses the bundled Graphology Leiden implementation by default. To test the #2337 Icebug migration path without changing default analyze behavior, set:

GITNEXUS_COMMUNITY_ENGINE=icebug npx gitnexus analyze

Supported values are graphology, icebug, and auto. The Icebug path is an experimental probe: GitNexus does not bundle an Icebug native package yet, and if a separately resolvable module is unavailable or its API does not match the expected Graph.fromCSR / ParallelLeidenView shape, analyze falls back to Graphology and reports the fallback in progress output. Today auto is behaviorally identical to icebug: both try Icebug and fall back to Graphology, while graphology skips the Icebug probe entirely.

MCP Tools

Your AI agent gets 17 tools (15 per-repo + 2 group) automatically:

Tool	What It Does
list_repos	Discover all indexed repositories (paginated — limit/offset)
query	Process-grouped hybrid search (BM25 + semantic + RRF)
context	360-degree symbol view — categorized refs, process participation
impact	Blast radius analysis with depth grouping and confidence
trace	Shortest directed path between two symbols (call + class-member edges)
detect_changes	Git-diff impact — maps changed lines to affected processes
check	Read-only structural checks against the indexed graph
rename	Multi-file coordinated rename with graph + text search
cypher	Raw Cypher graph queries
route_map	API route map — which components fetch which endpoints, and handlers
tool_map	MCP/RPC tool definitions — where they're defined and handled
shape_check	Validate API response shapes against consumers' property accesses
api_impact	Pre-change impact report for an API route handler
explain	Explain persisted taint findings (source→sink flows, --pdg indexes)
pdg_query	Query control/data dependence at statement level (--pdg indexes)
group_list	List configured repository groups
group_sync	Rebuild a group's Contract Registry and cross-repo links

With one indexed repo, the repo param is optional. With multiple, specify which: query({search_query: "auth", repo: "my-app"}). Per-repo tools also take an optional branch for indexes pinned with gitnexus analyze --branch; omitting it queries the workspace index, which follows your checked-out working tree. explain and pdg_query need an index built with gitnexus analyze --pdg.

MCP Resources

Resource	Purpose
gitnexus://repos	List all indexed repositories (read first)
gitnexus://setup	Setup and usage guidance for agents
gitnexus://repo/{name}/context	Codebase stats, staleness check, and available tools
gitnexus://repo/{name}/clusters	All functional clusters with cohesion scores
gitnexus://repo/{name}/cluster/{name}	Cluster members and details
gitnexus://repo/{name}/processes	All execution flows
gitnexus://repo/{name}/process/{name}	Full process trace with steps
gitnexus://repo/{name}/schema	Graph schema for Cypher queries
gitnexus://group/{name}/contracts	A group's extracted contracts and cross-links
gitnexus://group/{name}/status	Staleness of repos in a group

MCP Prompts

Prompt	What It Does
detect_impact	Pre-commit change analysis — scope, affected processes, risk level
generate_map	Architecture documentation from the knowledge graph with mermaid diagrams

CLI Commands

gitnexus setup                   # Configure MCP for detected editors (one-time; use -c to select)
gitnexus uninstall               # Preview removal of GitNexus MCP/skills/hooks (add --force to apply)
gitnexus analyze [path]          # Index a repository (or update stale index)
gitnexus analyze --repair-fts    # Fast path: rebuild/verify only FTS indexes on existing index data
gitnexus analyze --force         # Full rebuild: re-parse + graph rebuild + FTS rebuild
gitnexus analyze --embeddings    # Enable embedding generation (slower, better search)
gitnexus embeddings install      # Fetch the optional local embedding stack on demand (--cuda, --force)
gitnexus analyze --skills        # Generate repo-specific skill files from detected communities
gitnexus analyze --skip-agents-md  # Preserve custom AGENTS.md/CLAUDE.md gitnexus section edits
gitnexus analyze --skip-skills   # Skip installing standard .claude/skills/gitnexus-* skill files
gitnexus analyze --skip-git      # Index folders that are not Git repositories
gitnexus analyze --workers <n>   # Parse worker pool size (>=1; default: cores-1, capped at 16)
gitnexus analyze --verbose       # Log skipped files when parsers are unavailable
gitnexus analyze --max-file-size 1024  # Skip files larger than N KB (default: 512, cap: 32768)
gitnexus analyze --worker-timeout 60  # Increase worker idle timeout for slow parses
gitnexus analyze --wal-checkpoint-threshold 67108864  # 64 MiB. Control LadybugDB WAL auto-checkpoint threshold (default: 67108864 = 64 MiB; -1 keeps Ladybug stock ~16 MiB)
gitnexus mcp                     # Start MCP server (stdio) — serves all indexed repos
gitnexus serve                   # Start local HTTP server (multi-repo) for web UI
gitnexus index                   # Register an existing .gitnexus/ folder into the global registry
gitnexus list                    # List all indexed repositories
gitnexus status                  # Show index status for current repo
gitnexus clean                   # Delete index for current repo
gitnexus clean --all --force     # Delete all indexes
gitnexus wiki [path]             # Generate LLM-powered docs from knowledge graph
gitnexus wiki --model <model>    # Wiki with custom LLM model (default: minimax/minimax-m2.5)
gitnexus wiki --base-url http://llama-box.local:8080/v1 --allow-insecure-connection llama-box.local
                                  # Allow an exact LAN/self-hosted HTTP LLM host; env: GITNEXUS_ALLOW_INSECURE_CONNECTION
gitnexus doctor                  # Show runtime platform capabilities and embedding configuration

# Direct graph queries — the same tools the MCP server exposes, no MCP daemon needed
gitnexus query "<concept>"                                    # Process-grouped hybrid search
gitnexus context <symbol> [--uid <uid> | --file <path>]       # 360° symbol view; flags disambiguate a shared name
gitnexus impact <symbol> [--uid <uid> | --file <path> | --kind <kind>]  # Blast radius; flags disambiguate a shared name
gitnexus trace <from> <to>       # Shortest directed path between two symbols
gitnexus detect-changes          # Map the working-tree diff to affected symbols and execution flows
gitnexus check                   # Read-only structural checks against the indexed graph
gitnexus cypher "<query>"        # Run a raw Cypher query against the knowledge graph

# Repository groups (multi-repo / monorepo service tracking)
gitnexus group create <name>                                   # Create a repository group
gitnexus group add <group> <groupPath> <registryName>          # Add a repo to a group. <groupPath> is a hierarchy path (e.g. hr/hiring/backend); <registryName> is the repo's name from the registry (see `gitnexus list`)
gitnexus group remove <group> <groupPath>                      # Remove a repo from a group by its hierarchy path
gitnexus group list [name]                                     # List groups, or show one group's config
gitnexus group sync <name>                                     # Extract contracts and match across repos/services
gitnexus group contracts <name>  # Inspect extracted contracts and cross-links
gitnexus group query <name> <q>  # Search execution flows across all repos in a group
gitnexus group status <name>     # Check staleness of repos in a group
gitnexus group impact <name> --target <symbol> --repo <groupPath>  # Cross-repo blast radius

gitnexus uninstall reverses gitnexus setup — it removes the GitNexus MCP entries, hooks, and skill directories it added to each detected editor. Skill directories are identified by bundled gitnexus skill name (e.g. gitnexus-cli/), so if you customized files inside an installed skill directory, back them up first. It is a dry-run preview by default and prints the exact paths it would remove; pass --force to apply. Per-repo indexes (gitnexus clean --all) and the global npm package (npm uninstall -g gitnexus) are left for you to remove.

Remote Embeddings

Set these env vars to use a remote OpenAI-compatible /v1/embeddings endpoint instead of the local model:

export GITNEXUS_EMBEDDING_URL=http://your-server:8080/v1
export GITNEXUS_EMBEDDING_MODEL=BAAI/bge-large-en-v1.5
export GITNEXUS_EMBEDDING_DIMS=1024          # optional, default 384
export GITNEXUS_EMBEDDING_API_KEY=your-key   # optional, default: "unused"
export GITNEXUS_EMBEDDING_MAX_ATTEMPTS=3     # optional, total attempts (1-20)
export GITNEXUS_EMBEDDING_RETRY_CAP_MS=5000  # optional, maximum retry delay
export GITNEXUS_EMBEDDING_MIN_INTERVAL_MS=0  # optional, minimum request spacing
gitnexus analyze . --embeddings

Works with Infinity, vLLM, TEI, llama.cpp, Ollama, LM Studio, or OpenAI. Retry and pacing settings are provider-neutral; provider-specific limits should be supplied through configuration. When unset, local embeddings are used unchanged.

Multi-Repo Support

GitNexus supports indexing multiple repositories. Each gitnexus analyze registers the repo in a global registry (~/.gitnexus/registry.json). The MCP server serves all indexed repos automatically.

Supported Languages

TypeScript, JavaScript, Python, Java, C, C++, C#, Go, Rust, PHP, Kotlin, Swift, Ruby, Dart

Language Feature Matrix

Language	Imports	Named Bindings	Exports	Heritage	Type Annotations	Constructor Inference	Config	Frameworks	Entry Points
TypeScript	✓	✓	✓	✓	✓	✓	✓	✓	✓
JavaScript	✓	✓	✓	✓	—	✓	✓	✓	✓
Python	✓	✓	✓	✓	✓	✓	✓	✓	✓
Java	✓	✓	✓	✓	✓	✓	—	✓	✓
Kotlin	✓	✓	✓	✓	✓	✓	—	✓	✓
C#	✓	✓	✓	✓	✓	✓	✓	✓	✓
Go	✓	—	✓	✓	✓	✓	✓	✓	✓
Rust	✓	✓	✓	✓	✓	✓	—	✓	✓
PHP	✓	✓	✓	—	✓	✓	✓	✓	✓
Ruby	✓	—	✓	✓	—	✓	—	✓	✓
Swift	—	—	✓	✓	✓	✓	✓	✓	✓
C	—	—	✓	—	✓	✓	—	✓	✓
C++	—	—	✓	✓	✓	✓	—	✓	✓
Dart	✓	—	✓	✓	✓	✓	—	✓	✓

Imports — cross-file import resolution · Named Bindings — import { X as Y } / re-export tracking · Exports — public/exported symbol detection · Heritage — class inheritance, interfaces, mixins · Type Annotations — explicit type extraction for receiver resolution · Constructor Inference — infer receiver type from constructor calls (self/this resolution included for all languages) · Config — language toolchain config parsing (tsconfig, go.mod, etc.) · Frameworks — AST-based framework pattern detection · Entry Points — entry point scoring heuristics

Agent Skills

GitNexus ships with skill files that teach AI agents how to use the tools effectively:

• Exploring — Navigate unfamiliar code using the knowledge graph
• Debugging — Trace bugs through call chains
• Impact Analysis — Analyze blast radius before changes
• Refactoring — Plan safe refactors using dependency mapping
• Guide — GitNexus tool/resource/schema reference for the agent
• CLI — Run analyze/status/clean/wiki commands on request
• PDG Query — Statement-level control/data dependence queries (--pdg index)
• Taint Analysis — Source→sink data-flow findings (--pdg index)
• Plan / Work / Review / LFG — The engineering family: implementation-ready plans, gated plan execution, graph-backed change review with taint + expert lenses, and the end-to-end pipeline

Installed automatically by both gitnexus analyze (per-repo) and gitnexus setup (global). Run gitnexus analyze --skills to additionally generate each detected functional area as a direct project skill under .claude/skills/gitnexus-area-<name>/.

Requirements

• Node.js >= 22
• Git repository (uses git for commit tracking)

Release candidates

Stable releases publish to the default latest dist-tag. When a pull request with non-documentation changes merges into main, an automated workflow also publishes a prerelease build under the rc dist-tag, so early adopters can try in-flight fixes without waiting for the next stable cut. (Docs-only merges are skipped.)

# Try the latest release candidate (pre-stable — may change at any time)
npm install -g gitnexus@rc
# — or —
npx gitnexus@rc analyze

Release-candidate versions follow the standard semver prerelease format X.Y.Z-rc.N, where X.Y.Z is the next stable target (bumped from the current latest by patch by default; minor or major when kicking off a bigger cycle) and N increments per published rc. Example sequence: 1.6.2-rc.1, 1.6.2-rc.2, …, then once 1.6.2 ships stable, 1.6.3-rc.1. See the Releases page for the full list; stable latest is unaffected.

Troubleshooting

Cannot destructure property 'package' of 'node.target' as it is null

This error comes from npm 11.x's arborist while installing gitnexus (often via npx), before gitnexus code runs. It is triggered by platform-filtered optionalDependencies in native packages such as onnxruntime-node / @huggingface/transformers (used when indexing with --embeddings). GitNexus cannot catch it at runtime — use one of these workarounds:

pnpm --allow-build=@ladybugdb/core --allow-build=gitnexus --allow-build=tree-sitter dlx gitnexus@latest analyze       # auto-selected when pnpm + npm 11+
npm install -g gitnexus@latest         # global install avoids per-run npx reify
gitnexus analyze                       # if already installed globally

On pnpm 10+, lifecycle scripts are blocked unless explicitly allowed — the resolver adds --allow-build for @ladybugdb/core, gitnexus, and tree-sitter automatically when it picks pnpm dlx.

If you must stay on npm 11.x without pnpm, downgrade npm toolchain-wide (last resort):

npm install -g npm@10.9.0

See #1939 and the original #819 thread. An older variant of this crash (tree-sitter-dart tarball URL) was fixed in gitnexus v1.6.2+ (#820); if you still see install failures after upgrading, clear cache:

npm cache clean --force
npx gitnexus@latest analyze

ERR_DLOPEN_FAILED / lbugjs.node missing (pnpm dlx, pnpx)

GitNexus depends on @ladybugdb/core, whose native database addon (lbugjs.node) is placed by a postinstall script. pnpm dlx, pnpx, and any install run with --ignore-scripts skip lifecycle scripts, so the addon is never put in place and the runtime crashes with ERR_DLOPEN_FAILED:

Error: dlopen(.../@ladybugdb/core/lbugjs.node, ...): tried: '...' (no such file)
  code: 'ERR_DLOPEN_FAILED'

Options that run install scripts:

# pnpm dlx with explicit build permission (one-off, no global install required)
pnpm --allow-build=@ladybugdb/core --allow-build=gitnexus --allow-build=tree-sitter \
  dlx gitnexus@latest serve

# npm: global install (recommended on npm 11+; bare npx may crash — see section above)
npm install -g gitnexus@latest
gitnexus serve

# npx (npm < 11, or after upgrading npm)
npx gitnexus@latest serve

# pnpm: global install with build scripts allowed (pnpm 10.2+; no approve-builds -g on pnpm 11+)
pnpm add -g --allow-build=@ladybugdb/core --allow-build=gitnexus --allow-build=tree-sitter gitnexus
gitnexus serve

Installation fails with native module errors

Some optional language grammars (Dart, Proto, Swift, Kotlin) require native compilation. If they fail, GitNexus still works — those languages will be skipped. To skip them intentionally (no C++ toolchain needed), set GITNEXUS_SKIP_OPTIONAL_GRAMMARS=1 before installing.

If npm install -g gitnexus fails on native modules:

# Ensure build tools are available (Linux/macOS)
# Ubuntu/Debian: sudo apt install python3 make g++
# macOS: xcode-select --install

# Retry installation
npm install -g gitnexus

Installation fails behind an HTTP proxy (onnxruntime-node postinstall)

onnxruntime-node's postinstall downloads optional CUDA GPU binaries from api.nuget.org — outside the npm registry, so registry mirrors don't cover it, and its proxy layer (global-agent) ignores the standard HTTP_PROXY/HTTPS_PROXY variables and rejects 302 redirects (#2370).

Since the packages are optional dependencies, a failed download no longer breaks npm install -g gitnexus — npm skips the embedding stack and everything else works. The stack then self-heals on demand: the first gitnexus analyze --embeddings (or an explicit gitnexus embeddings install) fetches it through your configured npm registry — mirrors and proxies apply, no NuGet download involved — into ~/.gitnexus/embedding-runtime.

# heal a proxy-degraded install manually (CPU embeddings; registry-only)
gitnexus embeddings install

# reinstall into the prefix even when the stack already resolves
gitnexus embeddings install --force

# CUDA GPU hosts: also fetch GPU binaries (NuGet; set the proxy global-agent reads)
GLOBAL_AGENT_HTTPS_PROXY=<proxy-url> gitnexus embeddings install --cuda

The prefix defaults to ~/.gitnexus/embedding-runtime; set GITNEXUS_EMBEDDING_RUNTIME_DIR to install it elsewhere (e.g. a writable path in a container).

Node requirement for the on-demand prefix: the self-heal loads the prefixed packages via module.registerHooks, available on Node ≥ 22.15 (on the 22.x line) or ≥ 23.5 (on the 23.x line). On an older Node the packages install but can't be loaded from the prefix — reinstall them into the install itself instead (works on every supported Node): ONNXRUNTIME_NODE_INSTALL=skip npm install -g gitnexus (Windows: set ONNXRUNTIME_NODE_INSTALL=skip && npm install -g gitnexus). Skipping only the CUDA download keeps full CPU embeddings (CPU embeddings don't need it). Check the result any time with gitnexus doctor (Embeddings → Support line).

Analyze warns about unavailable FTS or VECTOR extensions

GitNexus uses optional DuckDB extensions for BM25 and vector search. The gitnexus serve and MCP read paths only ever try to LOAD the extensions — they never block on a network install. The analyze command, by default, attempts one bounded out-of-process install if LOAD fails (a plain INSTALL to download a missing extension, escalating to FORCE INSTALL only when the LOAD error shows the existing file is broken or truncated, so a permanent non-file failure does not re-download on every run) and proceeds even when that install times out, so the index is always written to disk; BM25/vector search degrade gracefully until the extensions become available.

Configure the behavior with these environment variables:

Variable	Values	Default	Effect
GITNEXUS_LBUG_EXTENSION_INSTALL	auto, load-only, never	auto	auto runs one bounded install if LOAD fails — a plain INSTALL, escalating to FORCE INSTALL only when the LOAD error shows the present extension file is broken. load-only only uses already-installed extensions (recommended for offline / firewalled environments). never skips optional extensions entirely.
GITNEXUS_LBUG_EXTENSION_INSTALL_TIMEOUT_MS	positive integer	15000	Wall-clock budget for the out-of-process extension-install child before it is killed.
GITNEXUS_FTS_STEMMER	supported LadybugDB stemmer	porter	Stemmer used when rebuilding BM25/FTS indexes. Use none for CJK-heavy repositories, or a language stemmer such as german, french, or spanish when that better matches repository comments and identifiers. Re-run gitnexus analyze --repair-fts after changing it.
GITNEXUS_FTS_CJK_SEGMENTATION	none, bigram	none	bigram inserts overlapping character-bigram boundaries into Chinese/Japanese Han-ideograph spans in content/description before FTS indexing, so LadybugDB's space-only tokenizer can see sub-phrase word boundaries. Scoped to CJK Unified Ideographs only — Japanese Hiragana/Katakana and Korean Hangul are not currently segmented. Unlike GITNEXUS_FTS_STEMMER, this rewrites stored text — enabling it on an already-indexed repo requires a full gitnexus analyze --force; neither --repair-fts nor a plain incremental analyze applies it to previously-indexed files. Set the same value wherever analyze and search-serving processes (CLI query, MCP server, web server) run.
GITNEXUS_COMMUNITY_ENGINE	graphology, icebug, auto	graphology	Community-detection engine used during analyze. graphology uses the bundled default path. icebug and auto currently behave identically: both try the experimental Icebug CSR path and fall back to Graphology if the optional native module is unavailable or incompatible.
GITNEXUS_WAL_CHECKPOINT_THRESHOLD	integer >= -1	67108864 (64 MiB)	LadybugDB WAL auto-checkpoint threshold during analyze (bytes). Auto-checkpoint remains enabled; -1 keeps Ladybug's stock ~16 MiB. Larger thresholds reduce checkpoint frequency but increase the WAL size at rotation time — choose a smaller value on disk-constrained environments.
GITNEXUS_LBUG_BUFFER_POOL_SIZE	integer >= 0 (bytes)	min(2 GiB, 80% RAM)	LadybugDB buffer-pool ceiling for every GitNexus database (analyze, MCP server, serve, group bridges). Bounded so a long-lived gitnexus mcp process or a large incremental analyze cannot grow toward LadybugDB's native 80%-of-RAM default and OOM the host (#2557). 0 restores that native unbounded default; invalid values warn and fall back to the default.
GITNEXUS_LBUG_MAX_DB_SIZE	positive integer (bytes)	17179869184 (16 GiB)	Upper bound for a single LadybugDB database file. This is an mmap/disk-address-space ceiling, not a memory limit — it does not constrain the buffer pool (use GITNEXUS_LBUG_BUFFER_POOL_SIZE for that). Raise it when indexing genuinely huge monorepos; invalid values silently fall back to the default.

# Offline/airgapped: never reach the network for extensions
GITNEXUS_LBUG_EXTENSION_INSTALL=load-only npx gitnexus analyze

# Slow network: give extension downloads more time
GITNEXUS_LBUG_EXTENSION_INSTALL_TIMEOUT_MS=30000 npx gitnexus analyze

# CJK-heavy codebase: rebuild keyword indexes without English stemming
GITNEXUS_FTS_STEMMER=none npx gitnexus analyze --repair-fts

# CJK-heavy codebase: enable sub-phrase search over Chinese/Japanese Han text.
# On an already-indexed repo, the first run after enabling this MUST be --force —
# --repair-fts and plain incremental `analyze` both leave old files un-segmented.
GITNEXUS_FTS_CJK_SEGMENTATION=bigram npx gitnexus analyze --force

Analysis runs out of memory

For very large repositories:

# Increase Node.js heap size
NODE_OPTIONS="--max-old-space-size=16384" npx gitnexus analyze

# Exclude large directories
echo "vendor/" >> .gitnexusignore
echo "dist/" >> .gitnexusignore

Large files are being skipped

By default the walker skips files larger than 512 KB (see log line Skipped N large files (>512KB)). Raise the threshold via either the CLI flag or the environment variable — both accept a value in KB:

# CLI flag (takes precedence over the env var)
npx gitnexus analyze --max-file-size 2048     # skip only files > 2 MB

# Environment variable (persists across commands)
export GITNEXUS_MAX_FILE_SIZE=2048
npx gitnexus analyze

Values above 32768 KB (32 MB) are clamped to the tree-sitter parser ceiling; invalid values fall back to the 512 KB default with a one-time warning. When an override is active, analyze prints the effective threshold in its startup banner (e.g. GITNEXUS_MAX_FILE_SIZE: effective threshold 2048KB (default 512KB)).

Analyze reports a worker timeout

Worker parse timeouts are recoverable. GitNexus retries stalled worker jobs with backoff, splits large jobs to isolate slow files, and quarantines a file that repeatedly crashes its worker (respawning the slot so the pool keeps going). If a large repository needs more time per worker job, use either:

# CLI flag, in seconds
npx gitnexus analyze --worker-timeout 60

# Environment variable, in milliseconds
export GITNEXUS_WORKER_SUB_BATCH_TIMEOUT_MS=60000
npx gitnexus analyze

For repositories with very large source files, GITNEXUS_WORKER_SUB_BATCH_MAX_BYTES controls the worker job byte budget. The default is 8388608 bytes (8 MB).

Worker pool resilience tuning

Three env vars expose the pool's resilience layers (respawn budget, cumulative-timeout cap, circuit breaker). Defaults are tuned for typical repos; bump them when an analyze legitimately needs more retries, or lower them to fail-fast on a known-bad shape.

Variable	Default	Effect
GITNEXUS_WORKER_MAX_RESPAWNS_PER_SLOT	3	Max replacement spawns per slot before the slot is dropped from the active rotation.
GITNEXUS_WORKER_MAX_CUMULATIVE_TIMEOUT_MS	5 × subBatchTimeoutMs	Total retry wall-time budget per job before quarantining. Bounds exponentially-growing retry waits.
GITNEXUS_WORKER_CONSECUTIVE_FAILURE_THRESHOLD	max(3, poolSize)	Per-slot consecutive deaths before the pool's circuit breaker trips. After tripping, dispatches require a fresh pool.
GITNEXUS_WORKER_SHUTDOWN_DRAIN_MS	30000	Max wait at pool shutdown for a retired worker still inside native code — terminated at its next JS-safe point instead of mid-native-call, which would abort the process (Napi::Error, #2432).
GITNEXUS_CPP_CAPTURE_BUDGET_MS	20000	Per-file wall-clock budget for C++ capture extraction; on breach the file keeps partial captures with a warning (#2432). 0 expires immediately.

Graph cleanup tuning

After scope resolution, analyze prunes inert block-local value symbols (a function-local const/let/var that ends up with only its structural File→DEFINES edge) to keep the graph focused on cross-symbol relationships. Module/file-scope symbols, class members, and any local with a real edge are always kept.

Variable	Default	Effect
GITNEXUS_KEEP_LOCAL_VALUE_SYMBOLS	unset	Set to 1/true to keep inert block-local value symbols instead of pruning them.

Programmatic callers can pass keepLocalValueSymbols: true in PipelineOptions instead of setting the env var.

Hook augmentation and skip diagnostics

The Claude Code / Antigravity hooks keep their stderr silent on normal skip paths so strict hook runners (e.g. Codex PreToolUse) never see unexpected diagnostic output.

When a GitNexus process holds the repo DB write lock (the common case — the MCP server is running, or the DB-lock probe timed out and failed closed), the local CLI augment can't run (LadybugDB is single-writer). Rather than drop the augmentation, the hook hands the agent a short, conditional MCP-query hint on stdout (the sanctioned additionalContext channel) — "if the GitNexus MCP tools are live in this session, call query …" — so an agent that has the tools can still fetch graph-ranked context. The hint is throttled to at most once per repo per window (GITNEXUS_MCP_HINT_THROTTLE_MS, default 10 min; 0 disables), so an owner-locked session isn't nudged on every search. A stale-index reminder, or an already-current index, stays silent.

To see why a hook skipped the CLI augment, set GITNEXUS_DEBUG=1 and re-run the action — the hook writes the reason (e.g. [GitNexus] augment skipped: MCP server owns DB) and the stale-index hint to its stderr:

GITNEXUS_DEBUG=1 <your command>   # surfaces hook skip/diagnostic reasons on stderr

Only GITNEXUS_DEBUG=1 and GITNEXUS_DEBUG=true enable diagnostics; every other value (including 0 and false) is treated as off. Diagnostics go to stderr only — the hook's structured stdout (the JSON the agent consumes) is unaffected.

Privacy

• All processing happens locally on your machine
• No code is sent to any server
• Index stored in .gitnexus/ inside your repo (gitignored)
• Global registry at ~/.gitnexus/ stores only paths and metadata

Web UI

GitNexus also has a browser-based UI at gitnexus.vercel.app — 100% client-side, your code never leaves the browser.

Local Backend Mode: Run gitnexus serve and open the web UI locally — it auto-detects the server and shows all your indexed repos, with full AI chat support. No need to re-upload or re-index. The agent's tools (Cypher queries, search, code navigation) route through the backend HTTP API automatically.

License

PolyForm Noncommercial 1.0.0

Free for non-commercial use. Contact for commercial licensing.