Gitnexus Guide

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. On query / context / impact / cypher, read staleness.status and staleness.branch/lastCommit before using the answer. Re-analyze only for behind or diverged.

Skills

Tools Reference

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 truelist_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.

Inline staleness signal (query / context / impact / cypher)

These four hot read tools attach a non-blocking staleness field to every response, in the shape { status, branch?, lastCommit, indexedAt, measuredAgainst, commitsBehind?, hint? }. It answers two different questions at once: which index answered and how fresh it is. The identity half is why the field is present even when nothing is wrong — an answer computed from a branch-pinned index is otherwise indistinguishable from one computed from the default branch (#3291):

{ /* …the tool's normal result… */  "staleness": {    "status": "current",    "branch": "feature/checkout-v2",    "lastCommit": "4f2a1c9e8b7d6a5c4e3f2a1b0c9d8e7f6a5b4c3d",    "indexedAt": "2026-09-15T07:12:00.000Z",    "measuredAgainst": "HEAD"  }}

status: "current" here means this index is at the HEAD of the clone it was built from — not that it is current with the default branch. measuredAgainst names what commitsBehind is counted against: the checked-out HEAD of that clone, never the remote. branch is the branch the index represents; it is absent for a detached HEAD, a non-git folder, or a legacy index that never recorded one, so read lastCommit when you need an identifier that is always present.

When the index is behind that HEAD, the count and hint ride along:

{ /* …the tool's normal result… */  "staleness": {    "status": "behind", "commitsBehind": 3, "branch": "main",    "lastCommit": "a0c945022d06b8815f93ffd8838df9ed5c08cbc0",    "indexedAt": "2026-09-04T20:45:47.481Z", "measuredAgainst": "HEAD",    "hint": "⚠️ Index is 3 commits behind HEAD. Run analyze tool to update."  }}

commitsBehind is present only when git counted the gap. When git could not count it but HEAD still resolves to a commit other than the indexed one — usually because the indexed commit is no longer in the clone's history — the index is provably not at HEAD with no countable gap, so no number is reported:

{ /* …the tool's normal result… */  "staleness": {    "status": "diverged", "branch": "main",    "lastCommit": "a0c945022d06b8815f93ffd8838df9ed5c08cbc0",    "indexedAt": "2026-09-04T20:45:47.481Z", "measuredAgainst": "HEAD",    "hint": "⚠️ Index is not at HEAD and the commit gap could not be counted — the recorded commit may no longer be in this clone's history. Run analyze tool to update."  }}

So: read status before using commitsBehind, and read branch/lastCommit before assuming which ref the answer describes. status: "unknown" means the freshness check could not run at all (a --skip-git folder has no history to measure) — the ref is still reported, because which index answered is knowable even when its freshness is not. The field is only ever added to object results — raw-array cypher output and error envelopes are returned unchanged. @group-targeted calls do not carry it (multi-repo staleness is ill-defined). Re-run analyze only for behind or diverged — those mean the index is not at this clone's HEAD. unknown is unmeasurable, not stale; analyze cannot make it current unless git history exists.

list_repos and the HTTP repo routes are unchanged: they omit staleness entirely for a current index and report the ref through their own top-level branch / lastCommit / indexedAt fields.

Taint findings (explain)

explain returns taint findings recorded by gitnexus analyze --pdg — intra-procedural TAINTED edges plus cross-function TAINT_PATH hops where the interprocedural taint phase found a function-level source→sink chain. Each finding includes 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: closure/callback, property/field, and implicit flows are not modeled, and interprocedural findings are function-level TAINT_PATH hops rather than statement-level path proof, 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.

Cross-repo (experimental): pass repo: "@groupName" to trace across a group's member repos — the path may cross one ContractLink boundary (reported as a CONTRACT_LINK hop with the bridged contract in crossings[]). Omit to entirely to follow from's outgoing HTTP call to whatever provider endpoint it lands on. Groups are configured via group_list / group_sync.

Resources Reference

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

Graph Schema

Nodes: File, Folder, Function, Class, Interface, Method, CodeElement, Community, Process, Route, Tool, plus language-specific types (Struct, Enum, Trait, Impl, Namespace, Module, …) and BasicBlock (--pdg indexes only). The full node list lives in gitnexus://repo/{name}/schema. Edges (via CodeRelation.type): CALLS, IMPORTS, EXTENDS, IMPLEMENTS, DEFINES, CONTAINS, MEMBER_OF, HAS_METHOD, HAS_PROPERTY, ACCESSES, METHOD_OVERRIDES, METHOD_IMPLEMENTS, STEP_IN_PROCESS, HANDLES_ROUTE, FETCHES, HANDLES_TOOL, ENTRY_POINT_OF, WRAPS, QUERIES, INJECTS, plus --pdg-only types (CFG, REACHING_DEF, TAINTED, SANITIZES, TAINT_PATH, CDG — zero rows on a default index).

Read gitnexus://repo/{name}/schema before writing Cypher — it is the authoritative schema for the indexed repo.

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