GitNexus/gitnexus/skills/gitnexus-guide.md

name	description
gitnexus-guide	Use when the user asks about GitNexus itself — available tools, how to query the knowledge graph, MCP resources, graph schema, or workflow reference. Examples: "What GitNexus tools are available?", "How do I use GitNexus?"

GitNexus Guide

Quick reference for all GitNexus MCP tools, resources, and the knowledge graph schema.

Always Start Here

For any task involving code understanding, debugging, impact analysis, or refactoring:

1. Read gitnexus://repo/{name}/context — codebase overview + check index freshness
2. Match your task to a skill below and read that skill file
3. Follow the skill's workflow and checklist

If step 1 warns the index is stale, run node .gitnexus/run.cjs analyze in the terminal first.

Skills

Task	Skill to read
Understand architecture / "How does X work?"	gitnexus-exploring
Blast radius / "What breaks if I change X?"	gitnexus-impact-analysis
Trace bugs / "Why is X failing?"	gitnexus-debugging
Rename / extract / split / refactor	gitnexus-refactoring
Tools, resources, schema reference	gitnexus-guide (this file)
Index, status, clean, wiki CLI commands	gitnexus-cli

Tools Reference

Tool	What it gives you
query	Process-grouped code intelligence — execution flows related to a concept
context	360-degree symbol view — categorized refs, processes it participates in
impact	Symbol blast radius — what breaks at depth 1/2/3 with confidence
trace	Shortest path between two symbols — "how does A reach B?" in one call
detect_changes	Git-diff impact — what do your current changes affect
rename	Multi-file coordinated rename with confidence-tagged edits
cypher	Raw graph queries (read gitnexus://repo/{name}/schema first)
explain	Persisted taint findings — source→sink data flows (needs analyze --pdg)
pdg_query	Control/data dependence — what gates X (CDG) / where Y flows (REACHING_DEF); needs analyze --pdg
check	Check graph invariants such as circular imports
list_repos	Discover indexed repos (paginated — limit/offset)

Paginating list_repos

list_repos is paginated so a large registry is not truncated by MCP/LLM token limits. It takes optional limit (default 50, max 200) and offset, and returns:

{
  "repositories": [
    { "name": "...", "path": "...", "indexedAt": "...", "lastCommit": "...", "stats": { } }
  ],
  "pagination": {
    "total": 437,
    "limit": 50,
    "offset": 0,
    "returned": 50,
    "hasMore": true,
    "nextOffset": 50
  }
}

To enumerate every repository, keep calling with offset set to pagination.nextOffset until hasMore is false:

list_repos {}               → repos 1–50,    nextOffset 50,  hasMore true
list_repos { offset: 50 }   → repos 51–100,  nextOffset 100, hasMore true
…
list_repos { offset: 400 }  → repos 401–437,                 hasMore false   (done)

Notes: offset ≥ total returns an empty page (with total still reported). Out-of-range or malformed limit/offset (non-integer, limit outside [1, 200], offset < 0) are rejected with a clear error — limit above the max is rejected, not silently capped. The order is deterministic (lower-cased name, then path), so paging never skips or duplicates an entry while the registry is unchanged.

Taint findings (explain)

explain returns intra-procedural taint findings (TAINTED edges) recorded by gitnexus analyze --pdg — each with a sink category (command-injection, code-injection, path-traversal, sql-injection, xss), source/sink lines, and the ordered hop path with the variable carried on each hop.

• explain {} — enumerate all findings for the repo (bounded by limit, deterministic order)
• explain { target: "src/vuln.ts" } — findings in a file (suffix path match accepted)
• explain { target: "runUserCommand" } — findings in a function (resolved like context; ambiguous names return ranked candidates)

A repo indexed without --pdg returns a clear "no taint layer" note. Caveats: findings are intra-procedural only — cross-function, closure/callback, property/field, and implicit flows are not modeled, so the absence of a finding is not proof of safety. SANITIZES (sanitizer-kill) edges are queryable via cypher.

Control & data dependence (pdg_query)

pdg_query reads the control/data-dependence layers gitnexus analyze --pdg records (CDG + REACHING_DEF, basic-block granular) — the control/data analog of explain. It is always anchored (a target file path or symbol, resolved like context) and has two modes:

• pdg_query { mode: "controls", target: "..." } — CDG: "under what condition does X run?". Each edge is a controlling predicate block → dependent block with the branch sense ('T'/'F') in reason; an edge into an early return/throw is flagged guard: true (guard-clause discovery — the sense depends on the predicate, so don't filter guards by a fixed label).
• pdg_query { mode: "flows", target: "...", variable?: "..." } — REACHING_DEF def→use edges within the function; pass variable to trace one binding.

A repo indexed without --pdg returns a "no PDG layer" note (or "status unknown" when the layer can't be confirmed). Intra-procedural only — cross-function flow is taint's domain (explain). The raw CDG/REACHING_DEF edges are also queryable via cypher. See the gitnexus-pdg-query skill for the full query surface.

Shortest path between two symbols (trace)

trace answers "how does A reach B?" in one call — the shortest directed path over CALLS (plus HAS_METHOD, so a class-rooted trace descends into its methods) instead of chaining 3–8 context/impact hops by hand.

• trace { from: "validateUser", to: "executeQuery" } — shortest path between two symbols.
• Disambiguate common names with from_uid/to_uid (zero-ambiguity) or from_file/to_file; an ambiguous name returns ranked candidates.
• maxDepth (default 10, max 30) bounds the search; includeTests (default false) lets the traversal pass through test-file symbols.

Returns ordered hops (each { name, filePath, startLine }) and an aligned edges[] of { relType, confidence }, so call hops and containment (HAS_METHOD) hops stay distinguishable. When no path exists it reports the furthest reachable node (where the chain breaks) and sets truncated: true if a traversal cap was hit first. Every result carries a status: ok / no_path / ambiguous / not_found / error.

Resources Reference

Lightweight reads (~100-500 tokens) for navigation:

Resource	Content
gitnexus://repo/{name}/context	Stats, staleness check
gitnexus://repo/{name}/clusters	All functional areas with cohesion scores
gitnexus://repo/{name}/cluster/{clusterName}	Area members
gitnexus://repo/{name}/processes	All execution flows
gitnexus://repo/{name}/process/{processName}	Step-by-step trace
gitnexus://repo/{name}/schema	Graph schema for Cypher

Graph Schema

Nodes: File, Function, Class, Interface, Method, Community, Process Edges (via CodeRelation.type): CALLS, IMPORTS, EXTENDS, IMPLEMENTS, DEFINES, MEMBER_OF, STEP_IN_PROCESS

MATCH (caller)-[:CodeRelation {type: 'CALLS'}]->(f:Function {name: "myFunc"})
RETURN caller.name, caller.filePath