Refactoring with GitNexus

When to Use

• "Rename this function safely"
• "Extract this into a module"
• "Split this service"
• "Move this to a new file"
• Any task involving renaming, extracting, splitting, or restructuring code

Bind the repository first

Refactoring writes to disk. rename with dry_run: false edits files in whichever repository was resolved, so binding identity here is a safety gate, not bookkeeping.

Call list_repos {} before the first tool call. With one indexed repository, use the examples below as written. With more than one, pass repo on every call: an omitted repo normally errors, but under an MCP policy with a configured default it resolves to that default silently. If you cannot tell which repository is meant, stop and ask. Never run rename with dry_run: false until the preview in the same bound repository has been reviewed — its returned file_path values show which checkout is about to be written, so read them as a confirmation of identity.

list_repos is paginated, so page with offset: pagination.nextOffset until hasMore is false before concluding a repository is absent.

detect_changes takes worktree when you are editing a linked worktree the MCP server was not launched from; otherwise git diff runs in the wrong checkout and reports nothing changed, which reads as a verified refactor.

Workflow

0. list_repos {}                                  → Bind repo (and worktree)
1. impact({target: "X", direction: "upstream"})  → Map all dependents
2. query({search_query: "X"})                            → Find execution flows involving X
3. context({name: "X"})                           → See all incoming/outgoing refs
4. Plan update order: interfaces → implementations → callers → tests

If "Index is stale" → run node .gitnexus/run.cjs analyze in terminal.

Checklists

Rename Symbol

- [ ] list_repos {} — bind repo; explicit repo when >1 indexed, ask if ambiguous
- [ ] rename({symbol_name: "oldName", new_name: "newName", dry_run: true}) — preview all edits
- [ ] Confirm the previewed file paths are in the bound repository/worktree
- [ ] Review graph edits (high confidence) and text_search edits (review carefully)
- [ ] If satisfied: rename({..., dry_run: false}) — apply edits
- [ ] detect_changes() — verify only expected files changed
- [ ] Run tests for affected processes

Extract Module

- [ ] list_repos {} — bind repo; explicit repo when >1 indexed, ask if ambiguous
- [ ] context({name: target}) — see all incoming/outgoing refs
- [ ] impact({target, direction: "upstream"}) — find all external callers
- [ ] Define new module interface
- [ ] Extract code, update imports
- [ ] detect_changes() — verify affected scope
- [ ] Run tests for affected processes

Split Function/Service

- [ ] list_repos {} — bind repo; explicit repo when >1 indexed, ask if ambiguous
- [ ] context({name: target}) — understand all callees
- [ ] Group callees by responsibility
- [ ] impact({target, direction: "upstream"}) — map callers to update
- [ ] Create new functions/services
- [ ] Update callers
- [ ] detect_changes() — verify affected scope
- [ ] Run tests for affected processes

Tools

rename — automated multi-file rename:

rename({symbol_name: "validateUser", new_name: "authenticateUser", repo: "my-app", dry_run: true})
→ 12 edits across 8 files
→ 10 graph edits (high confidence), 2 text_search edits (review)
→ Changes: [{file_path, edits: [{line, old_text, new_text, confidence}]}]

impact — map all dependents first:

impact({target: "validateUser", repo: "my-app", direction: "upstream"})
→ d=1: loginHandler, apiMiddleware, testUtils
→ Affected Processes: LoginFlow, TokenRefresh

detect_changes — verify your changes after refactoring:

detect_changes({scope: "all"})
→ Changed: 8 files, 12 symbols
→ Affected processes: LoginFlow, TokenRefresh
→ Risk: MEDIUM

partial: true (a graph query failed) or truncated: true (the changed-symbol listing was capped) means the result is short of the truth: a short or empty list is not proof that only the expected files changed. Re-run it rather than treat the refactor as verified.

A wrong-worktree zero carries neither flag and is indistinguishable from a clean verification, so confirm the diffed checkout is the one you edited.

cypher — custom reference queries:

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

Risk Rules

Example: Rename validateUser to authenticateUser

0. list_repos {}
   → total: 2 (my-app, billing-api) — both define validateUser, so bind explicitly

1. rename({symbol_name: "validateUser", new_name: "authenticateUser", repo: "my-app", dry_run: true})
   → 12 edits: 10 graph (safe), 2 text_search (review)
   → Files: validator.ts, login.ts, middleware.ts, config.json...

2. Review text_search edits (config.json: dynamic reference!)

3. rename({symbol_name: "validateUser", new_name: "authenticateUser", repo: "my-app", dry_run: false})
   → Applied 12 edits across 8 files

4. detect_changes({scope: "all", repo: "my-app"})
   → Affected: LoginFlow, TokenRefresh
   → Risk: MEDIUM — run tests for these flows
   Repository: my-app (/abs/path/my-app)  Worktree: same  Index: current

With a single indexed repository, step 0 returns total: 1 and the repo argument drops out of every call above.