xtrm-tools 0.5.46 → 0.5.48

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Files changed (34) hide show
  1. package/.claude-plugin/plugin.json +1 -1
  2. package/README.md +5 -5
  3. package/cli/dist/index.cjs +9728 -9967
  4. package/cli/dist/index.cjs.map +1 -1
  5. package/cli/package.json +2 -1
  6. package/config/instructions/agents-top.md +2 -4
  7. package/config/instructions/claude-top.md +2 -4
  8. package/config/pi/extensions/beads/index.ts +18 -81
  9. package/config/pi/extensions/xtrm-ui/format.ts +93 -0
  10. package/config/pi/extensions/xtrm-ui/index.ts +725 -12
  11. package/hooks/beads-claim-sync.mjs +15 -96
  12. package/hooks/beads-gate-messages.mjs +2 -4
  13. package/hooks/beads-gate-utils.mjs +0 -18
  14. package/hooks/statusline.mjs +5 -3
  15. package/hooks/tsconfig-cache.json +2 -12
  16. package/package.json +1 -1
  17. package/plugins/xtrm-tools/.claude-plugin/plugin.json +1 -1
  18. package/plugins/xtrm-tools/hooks/beads-claim-sync.mjs +15 -96
  19. package/plugins/xtrm-tools/hooks/beads-gate-messages.mjs +2 -4
  20. package/plugins/xtrm-tools/hooks/beads-gate-utils.mjs +0 -18
  21. package/plugins/xtrm-tools/hooks/statusline.mjs +5 -3
  22. package/plugins/xtrm-tools/hooks/tsconfig-cache.json +2 -12
  23. package/plugins/xtrm-tools/skills/planning/SKILL.md +75 -20
  24. package/plugins/xtrm-tools/skills/test-planning/SKILL.md +257 -0
  25. package/plugins/xtrm-tools/skills/using-xtrm/SKILL.md +1 -1
  26. package/plugins/xtrm-tools/skills/xt-debugging/SKILL.md +149 -0
  27. package/plugins/xtrm-tools/skills/xt-end/SKILL.md +28 -0
  28. package/skills/planning/SKILL.md +75 -20
  29. package/skills/test-planning/SKILL.md +257 -0
  30. package/skills/using-xtrm/SKILL.md +1 -1
  31. package/skills/xt-debugging/SKILL.md +149 -0
  32. package/skills/xt-end/SKILL.md +28 -0
  33. package/plugins/xtrm-tools/skills/gitnexus-debugging/SKILL.md +0 -85
  34. package/skills/gitnexus-debugging/SKILL.md +0 -85
@@ -62,16 +62,33 @@ If the request is under 8 words or the scope is unclear, ask **one** clarifying
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  Use GitNexus and Serena to understand the landscape. No file edits.
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+ ### GitNexus-first protocol (mandatory when available)
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+
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  ```bash
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- # Find relevant execution flows
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+ # 1) Find relevant execution flows by concept
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  gitnexus_query({query: "<concept related to task>"})
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- # Understand a specific symbol
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+ # 2) Get full caller/callee/process context for likely symbols
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  gitnexus_context({name: "<affected symbol>"})
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- # Check blast radius before planning changes
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+ # 3) Assess blast radius before locking the implementation plan
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  gitnexus_impact({target: "<symbol to change>", direction: "upstream"})
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+ ```
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+
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+ ### Refactor planning checks (when rename/extract/move is in scope)
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+
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+ ```bash
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+ # Preview safe multi-file rename plan first
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+ gitnexus_rename({symbol_name: "<old>", new_name: "<new>", dry_run: true})
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+
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+ # Confirm context before extraction/split plans
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+ gitnexus_context({name: "<symbol to extract/split>"})
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+ gitnexus_impact({target: "<symbol to extract/split>", direction: "upstream"})
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+ ```
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+
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+ ### Serena symbol-level inspection (targeted reads)
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+ ```bash
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  # Map a file without reading all of it
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  get_symbols_overview("path/to/relevant/file.ts")
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@@ -79,11 +96,44 @@ get_symbols_overview("path/to/relevant/file.ts")
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  find_symbol("SymbolName", include_body=true)
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  ```
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+ ### Fallback when GitNexus MCP tools are unavailable
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+
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+ If MCP GitNexus tools are unavailable, use the GitNexus CLI first, then Serena symbol exploration if needed.
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+
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+ ```bash
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+ # Verify index freshness / repository indexing
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+ npx gitnexus status
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+ npx gitnexus list
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+
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+ # Concept and architecture exploration
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+ npx gitnexus query "<concept or symptom>" --limit 5
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+ npx gitnexus context "<symbolName>"
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+
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+ # Blast radius before committing to a plan
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+ npx gitnexus impact "<symbolName>" --direction upstream --depth 3
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+
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+ # If index is stale
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+ npx gitnexus analyze
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+ ```
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+
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+ Notes:
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+ - In this environment, `detect_changes` and `rename` are available via MCP tools, not GitNexus CLI subcommands.
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+ - If both MCP and CLI are unavailable, fall back to Serena search + symbols and state this explicitly in your plan output.
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+
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+ ```bash
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+ search_for_pattern("<concept or symbol>")
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+ get_symbols_overview("path/to/relevant/file.ts")
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+ find_symbol("<candidate symbol>", include_body=true)
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+ find_referencing_symbols("<symbol>", "path/to/file.ts")
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+ ```
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+
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  **Capture from exploration:**
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  - Which files/symbols will be affected
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+ - Which execution flows/processes are involved (from `gitnexus_query`/`gitnexus_context`)
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  - What existing patterns to follow (naming, structure, error handling)
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  - Any d=1 dependents that require updates when you change a symbol
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- - Risk level: if CRITICAL or HIGH → warn user before proceeding
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+ - Risk level from impact analysis: if CRITICAL or HIGH → warn user before proceeding
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+ - If GitNexus fallback path was used, explicitly call it out in the handoff
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  ---
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@@ -101,6 +151,7 @@ Think through the plan before writing any bd commands. Use structured CoT:
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  3. What are the dependencies? (what must be done before X can start?)
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  4. What can run in parallel? (independent tasks → no deps between them)
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  5. What are the risks? (complex areas, unclear spec, risky refactors)
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+ 6. What is the blast-radius summary from GitNexus? (direct callers, affected processes, risk level)
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  </thinking>
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  <plan>
@@ -244,7 +295,13 @@ test-planning will:
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  ## Phase 6 — Handoff
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- Present the board and transition to implementation:
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+ Present the board and transition to implementation.
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+
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+ Include a short **Architecture & Impact Summary** in your handoff message:
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+ - Key execution flows/processes involved
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+ - Top d=1 dependents to watch
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+ - Highest observed risk (LOW/MEDIUM/HIGH/CRITICAL)
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+ - Whether GitNexus-first or fallback exploration was used
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  ```bash
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  # Show the full board
@@ -292,30 +349,26 @@ Then begin work on the first task. The planning phase is complete.
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  ### Example 2 — Bug fix with investigation
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  <example>
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- <scenario>User: "bd close sometimes doesn't auto-commit"</scenario>
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+ <scenario>User: "bd close doesn't commit my changes"</scenario>
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  <exploration>
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- gitnexus_query({query: "bd close auto-commit"})
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+ gitnexus_query({query: "bd close commit workflow"})
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  → finds: beads-claim-sync.mjs, close event handler
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- find_symbol("handleClose", include_body=true)
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- → discovers: auto-commit only fires if tracked files changed, not untracked
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+ find_symbol("main", include_body=true)
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+ → discovers: bd close sets closed-this-session KV only; no git commit
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  </exploration>
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  <thinking>
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- Root cause identified: git commit -am skips untracked files.
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- Fix: check git ls-files --others before committing.
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- Risk: LOWonly beads-claim-sync.mjs changes.
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- Single task, no phases needed.
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+ bd close does NOT auto-commit (removed in xtrm-wr0o).
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+ Correct workflow: bd close <id>, then git add + git commit separately, then xt end.
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+ No issue needed this is expected behavior.
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  </thinking>
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  <bd_command>
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- bd create \
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- --title="Fix bd close auto-commit skips untracked new files" \
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- --description="Context: beads-claim-sync.mjs uses 'git commit -am' which skips
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- untracked files. Fix: add 'git ls-files --others --exclude-standard' check and
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- 'git add -A' scoped to expected paths before committing.
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- AC: [ ] auto-commit includes new untracked files [ ] existing behavior preserved"
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- --type=bug --priority=1
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+ # No issue needed — explain the correct workflow to the user:
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+ # 1. bd close <id> --reason="..." ← closes issue
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+ # 2. git add . && git commit -m "..." ← commit changes manually
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+ # 3. xt end ← push, PR, merge, worktree cleanup
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  </bd_command>
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  </example>
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@@ -343,6 +396,8 @@ Before presenting the plan to the user:
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  - [ ] Every issue has context / what / AC / notes
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  - [ ] Dependencies are correct (A blocks B when B needs A's output)
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  - [ ] No task is more than "one session" of work (split if needed)
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+ - [ ] GitNexus evidence captured (query/context/impact) or fallback path explicitly stated
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+ - [ ] If refactor scope exists, rename/extract safety checks were included in plan
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  - [ ] test-planning was invoked (or scheduled as next step)
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  - [ ] First implementation issue is ready to claim
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@@ -206,3 +206,260 @@ Agent closes a feature issue that was done ad-hoc. No test issue found. Agent:
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  2. Picks strategy
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  3. Creates test issue as child of same parent
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  4. Documents what to assert based on the actual code
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+
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+ ## Anti-Pattern Checklist
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+
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+ Run this checklist at both trigger points (planning and closure review). Flag any anti-patterns in the test issue description before closing.
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+
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+ ### 1. Assertion-free tests
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+ **Detect**: Test body calls functions/methods but has no `assert`, `expect`, or equivalent statement.
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+ **Fix**: Add at least one meaningful assertion. If the goal is "doesn't throw", assert that explicitly — `with pytest.raises(...)` or `expect(() => fn()).not.toThrow()`.
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+
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+ ### 2. Tautological assertions
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+ **Detect**: The assertion can only fail if the test framework itself is broken. E.g. `assert result == result`, `expect(true).toBe(true)`, asserting a value against the same expression used to produce it.
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+ **Fix**: Assert against a concrete expected value derived independently from the production code. If you can't state what the expected value is without running the code, the test has no falsifiable claim.
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+
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+ ### 3. Context leakage / shared mutable state
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+ **Detect**: Tests share module-level variables, database rows, file state, or global config without reset between runs. Symptoms: tests pass individually but fail in suite order.
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+ **Fix**: Use fixtures with setup/teardown (`beforeEach`/`afterEach`, pytest fixtures with function scope). Every test starts from a clean slate.
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+
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+ ### 4. Over-mocking internal collaborators
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+ **Detect**: Mocks are patching classes or functions that live in the same module under test — not external services. The test validates that internal wiring was called, not that the observable outcome is correct.
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+ **Fix**: Only mock at system boundaries (HTTP clients, file I/O, external services). Test internal collaborators by letting them run. If they're hard to instantiate, extract the pure logic and test that directly.
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+
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+ ### 5. Tests that cannot fail under realistic regressions
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+ **Detect**: Remove the core logic being tested and re-read the test — would it still pass? If yes, the test provides no protection. Common form: only testing the happy path of a function whose bug would only appear in error paths.
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+ **Fix**: Add at least one negative-path or edge-case assertion that would catch the most likely regression. Consult the implementation for obvious failure modes.
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+
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+ ## Priority Heuristics
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+
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+ Test issues inherit priority from their implementation issues with bounded adjustment. The table below gives the deterministic mapping.
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+
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+ | Implementation risk | Test issue priority | Examples |
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+ |---|---|---|
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+ | Security / auth / protocol compat | P0 (equal) | Auth token validation, schema migration safety, API contract |
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+ | Regression-critical boundary path | P0–P1 (equal) | Client URL routing, CLI exit codes used by external tooling |
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+ | High-business-impact core logic | P1 (equal or +0) | Pricing computations, session state transitions |
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+ | Standard domain logic | P2 (+0 or +1) | Config merge, output formatters, parsers |
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+ | Low-risk internals / non-critical adapters | P3 (+1) | Helper utilities, optional UI formatting |
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+ | Polish / test debt cleanup | P4 | Improving existing test coverage, test naming |
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+
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+ **Inheritance rule**: start from the implementation issue's priority. Apply +1 if the test is covering a well-understood path with low regression risk. Never go lower than P2 for boundary or shell layer tests — integration tests are load-bearing.
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+
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+ **Equal priority examples**:
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+ - Impl is P1 (auth endpoint) → test issue is P1 (auth contract test must ship with the feature)
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+ - Impl is P0 (critical fix) → test issue is P0 (regression test must land in same PR)
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+
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+ **+1 priority examples**:
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+ - Impl is P2 (output formatter) → test issue is P3 (unit tests are useful but not blocking)
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+ - Impl is P3 (optional config key) → test issue is P4 (test debt, tackle in cleanup)
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+
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+ ## Definition of Done Templates
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+
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+ Use these templates verbatim in test issue descriptions. Replace `<...>` placeholders.
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+
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+ ### Core layer DoD
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+
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+ ```
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+ Layer: core
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+ Strategy: <unit | property-based | example-based>
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+ Covers: <impl issue IDs>
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+
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+ Assertions required:
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+ - [ ] Positive path: <expected output for valid input>
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+ - [ ] Negative path: <expected error/output for invalid input>
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+ - [ ] Edge cases explicitly enumerated: <list: empty input, zero, max boundary, ...>
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+ - [ ] Invariants/properties included: <e.g. "result is always sorted", "output length == input length">
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+
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+ Fixture policy:
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+ - [ ] No shared mutable state between tests
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+ - [ ] Deterministic fixtures (no random, no time.now() without injection)
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+ - [ ] Each test constructs its own input independently
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+
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+ Done when: all assertions above are implemented and passing in CI.
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+ ```
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+
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+ ### Boundary layer DoD
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+
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+ ```
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+ Layer: boundary
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+ Strategy: <live-contract | recorded-fixture | mock (last resort)>
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+ Covers: <impl issue IDs>
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+
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+ Assertions required:
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+ - [ ] Schema/contract assertions: <field presence, types, required vs optional>
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+ - [ ] Error codes and retry/fallback: <e.g. 404→empty list, 500→raises ServiceError>
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+ - [ ] Drift-safe: assertions check field presence and types, not brittle internal structure
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+ - [ ] Live-first policy documented: <live | recorded-fixture | mock — reason for choice>
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+
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+ Done when: contract assertions pass against live service (or recorded fixture if live unavailable).
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+ Fallback documented in issue if live is not accessible.
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+ ```
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+
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+ ### Shell layer DoD
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+
301
+ ```
302
+ Layer: shell
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+ Strategy: integration (subprocess or function-level wiring test)
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+ Covers: <impl issue IDs>
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+
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+ Assertions required:
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+ - [ ] End-to-end observable outcomes: <what the user sees — output format, exit code>
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+ - [ ] Failure-mode UX: <error messages, non-zero exit codes, stderr vs stdout>
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+ - [ ] Cross-component wiring: <core + boundary are called and integrated correctly>
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+ - [ ] At least one real-data scenario (not mocked) if service is accessible
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+
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+ Done when: integration tests run against real components (not mocked internals) and cover
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+ both success and at least one failure path.
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+ ```
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+
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+ ## Critical-Path Coverage
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+
318
+ Do not frame test issues around coverage percentages. Frame them around critical paths and risk rationale.
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+
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+ Every test issue description must include a **critical path map**:
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+
322
+ ```
323
+ Critical paths covered:
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+ - <path 1 and risk rationale>
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+ - <path 2 and risk rationale>
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+
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+ Known deferred paths (with follow-up refs):
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+ - <path not covered yet> → follow-up: <bd issue ID or "to be created">
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+ ```
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+
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+ **Why**: a 90% line-coverage number says nothing about whether the one path that processes payments is tested. A critical path map forces explicit reasoning about what matters and what was skipped.
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+
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+ **What counts as a critical path**:
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+ - Any path that involves auth, money, data loss, or external contract compliance
335
+ - Any path exercised by the user-facing CLI commands described in the issue
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+ - Any path explicitly mentioned in the implementation issue's acceptance criteria
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+
338
+ **What to do with deferred paths**:
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+ - Document them — don't silently skip
340
+ - Create a follow-up test issue if the deferred path is P2 or higher risk
341
+ - Reference the follow-up issue ID in the current test issue's description
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+
343
+ ## Advisory vs Enforcement Boundary
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+
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+ This skill is advisory. It recommends test strategy, creates test issues, and flags anti-patterns. It does not block code execution or enforce pass/fail decisions — that is the job of hooks and quality gates.
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+
347
+ | Concern | Who owns it | How enforced |
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+ |---|---|---|
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+ | Test strategy selection (TDD vs contract vs unit) | This skill | Recommendation only |
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+ | Anti-pattern detection in test issues | This skill | Checklist in issue description |
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+ | Priority assignment | This skill | Heuristics table above |
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+ | DoD template in issue description | This skill | Template pasted into bd issue |
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+ | CI test pass/fail | quality-gates hook | PostToolUse hook blocks on test failures |
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+ | Test file lint/type correctness | quality-gates hook | ESLint + mypy on every edit |
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+ | Branch not mergeable without tests | Not enforced | Human review — no automated gate today |
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+ | Claiming work without test issue existing | Not enforced | Human judgment — skill creates test issue at closure if missing |
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+
358
+ **Example — advisory boundary in practice**:
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+
360
+ You are planning tests for `.14` (async HTTP client). This skill:
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+ - Classifies as boundary layer ✓
362
+ - Recommends live-contract tests ✓
363
+ - Creates a test issue with DoD template ✓
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+ - Flags if you try to describe tests that only mock the HTTP layer ✓ (anti-pattern 4)
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+
366
+ It does NOT:
367
+ - Block `.14` from closing if the test issue isn't done
368
+ - Fail the build if the test issue is open
369
+ - Require approval before the implementation is merged
370
+
371
+ The test issue is a tracked commitment, not a gate. Gating is opt-in via `bd dep` dependencies you set up during planning.
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+
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+ ## v1.1 Format Examples
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+
375
+ ### Example A — Planning phase, boundary + shell epic
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+
377
+ Epic: "Implement gitnexus MCP sync in xtrm install"
378
+
379
+ Children: `.1` (MCP config writer), `.2` (sync-on-install integration), `.3` (CLI `xtrm mcp` command)
380
+
381
+ Classification:
382
+ - `.1` → boundary (writes to `.mcp.json`, file I/O)
383
+ - `.2` → shell (orchestrates install flow)
384
+ - `.3` → shell (CLI command)
385
+
386
+ Test issues created:
387
+
388
+ ```
389
+ bd create "Test: MCP config writer — contract tests for .mcp.json output" \
390
+ -t task -p 2 --parent <epic> \
391
+ -d "Layer: boundary
392
+ Strategy: example-based (file I/O, no external service)
393
+ Covers: .1
394
+
395
+ Assertions required:
396
+ - [ ] Positive path: valid servers config produces correct .mcp.json structure
397
+ - [ ] Negative path: invalid server entry raises validation error
398
+ - [ ] Edge cases: empty servers list, duplicate server names, existing .mcp.json is merged not overwritten
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+ - [ ] Drift-safe: assert on field presence (name, command, args), not internal object identity
400
+
401
+ Critical paths covered:
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+ - gitnexus server entry written with correct stdio transport — risk: wrong transport breaks MCP
403
+ - existing user entries preserved during merge — risk: data loss
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+
405
+ Known deferred paths:
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+ - test with malformed existing .mcp.json → follow-up: to be created (P3)
407
+
408
+ Done when: all assertions pass, no shared state between tests."
409
+ ```
410
+
411
+ ```
412
+ bd create "Test: xtrm install MCP sync + xtrm mcp CLI — integration tests" \
413
+ -t task -p 2 --parent <epic> \
414
+ -d "Layer: shell
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+ Strategy: integration (subprocess)
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+ Covers: .2, .3
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+
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+ Assertions required:
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+ - [ ] End-to-end: xtrm install writes correct .mcp.json in temp project dir
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+ - [ ] CLI: xtrm mcp list outputs expected server names
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+ - [ ] Failure-mode: xtrm mcp add with duplicate name exits non-zero with clear error
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+ - [ ] Cross-component: install flow calls MCP writer with correct config
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+
424
+ Critical paths covered:
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+ - full install → .mcp.json present and readable by Claude Code — risk: MCP servers not available
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+ - CLI add + list roundtrip — risk: user cannot inspect installed servers
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+
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+ Known deferred paths:
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+ - test with no write permission on project dir → follow-up: to be created (P4)
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+
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+ Done when: integration tests run against real file system in temp dir, no mocked internals."
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+ ```
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+
434
+ ---
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+
436
+ ### Example B — Closure gate, core layer, implementation diverged
437
+
438
+ Closing `.22` (config merge logic). Existing test issue `.31` was written before implementation.
439
+
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+ What `.22` actually built:
441
+ - Added precedence chain: env > file > defaults (original plan had only file > defaults)
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+ - Added type coercion for boolean env vars ("true"/"false" → bool)
443
+ - Removed support for `.xtrm.yaml` (only `.xtrm/config.json` now)
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+
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+ Updated test issue `.31`:
446
+
447
+ ```
448
+ bd update xtrm-31 --notes "Scope updated after .22 completed:
449
+ + Add test: env var takes precedence over file config (new precedence chain)
450
+ + Add test: 'true'/'false' env vars coerced to bool correctly
451
+ + Add test: 'TRUE', '1', '0' edge cases for bool coercion
452
+ + Remove test: .xtrm.yaml loading (format removed in .22)
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+
454
+ Anti-pattern check:
455
+ - [ ] tautological: none detected
456
+ - [ ] over-mocking: env injection via monkeypatch only, no internal mocking
457
+ - [ ] shared state: each test resets env via fixture
458
+
459
+ Critical paths covered:
460
+ - env > file > defaults chain — risk: wrong precedence silently overrides user config
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+ - bool coercion — risk: 'false' string treated as truthy in Python
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+
463
+ Known deferred paths:
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+ - test with missing HOME dir (pathlib resolution edge case) → follow-up: xtrm-4x (P4)"
465
+ ```
@@ -78,7 +78,7 @@ gitnexus_impact({target: "parseComposeServices", direction: "upstream"})
78
78
  get_symbols_overview("hooks/init.ts") # map file
79
79
  find_symbol("parseComposeServices", include_body=True) # read just this
80
80
  replace_symbol_body("parseComposeServices", newBody) # Serena edit
81
- bd close bd-xyz --reason="Fix YAML parse edge case" # close + auto-commit
81
+ bd close bd-xyz --reason="Fix YAML parse edge case" # close issue
82
82
  xt end # push, PR, merge, cleanup
83
83
  ```
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+ ---
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+ name: xt-debugging
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+ description: Complete debugging workflow — error analysis, log interpretation, performance profiling, and GitNexus call-chain tracing. Use when investigating bugs, errors, crashes, or performance issues.
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+ ---
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+
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+ # xt-debugging
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+
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+ Systematic debugging using the GitNexus knowledge graph for call-chain tracing, combined with error analysis, log interpretation, and performance profiling.
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+
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+ ## When to Use
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+
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+ - "Why is this function failing?"
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+ - "Trace where this error comes from"
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+ - "This endpoint returns 500"
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+ - Investigating crashes, unexpected behavior, or regressions
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+ - Performance issues
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+ - Reading logs or stack traces
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+
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+ ---
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+
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+ ## Prerequisites
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+
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+ GitNexus must be indexed before starting. If you see "index is stale" or no results:
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+
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+ ```bash
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+ npx gitnexus analyze # re-index the repo (run this, then retry)
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+ npx gitnexus status # verify freshness
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+ ```
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+
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+ ---
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+
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+ ## Phase 1 — Triage
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+
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+ Understand the symptom before touching any code.
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+
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+ 1. Read the full error message and stack trace
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+ 2. Identify the suspect symbol (function, class, endpoint)
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+ 3. Check for regressions — what changed recently?
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+ ```
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+ gitnexus_detect_changes({scope: "compare", base_ref: "main"})
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+ ```
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+
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+ ---
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+
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+ ## Phase 2 — Knowledge Graph Investigation
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+
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+ ```
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+ 1. gitnexus_query({query: "<error text or symptom>"}) → Related execution flows + symbols
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+ 2. gitnexus_context({name: "<suspect>"}) → Callers, callees, process participation
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+ 3. READ gitnexus://repo/{name}/process/{processName} → Full step-by-step execution trace
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+ 4. gitnexus_cypher({...}) → Custom call chain if needed
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+ ```
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+
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+ ### Patterns by Symptom
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+
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+ | Symptom | Approach |
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+ |---------|----------|
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+ | Error message | `query` for error text → `context` on throw site |
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+ | Wrong return value | `context` on function → trace callees for data flow |
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+ | Intermittent failure | `context` → look for external calls, async deps, race conditions |
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+ | Performance issue | `context` → find hot-path symbols with many callers |
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+ | Recent regression | `detect_changes` to see what changed |
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+
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+ ### Example — "Payment endpoint returns 500 intermittently"
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+
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+ ```
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+ 1. gitnexus_query({query: "payment error handling"})
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+ → Processes: CheckoutFlow, ErrorHandling
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+ → Symbols: validatePayment, handlePaymentError
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+
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+ 2. gitnexus_context({name: "validatePayment"})
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+ → Outgoing calls: verifyCard, fetchRates (external API!)
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+
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+ 3. READ gitnexus://repo/my-app/process/CheckoutFlow
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+ → Step 3: validatePayment → calls fetchRates (external, no timeout)
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+
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+ 4. Root cause: fetchRates has no timeout → intermittent failures under load
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+ ```
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+
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+ ---
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+
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+ ## Phase 3 — Root Cause Analysis
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+
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+ 1. **Reproduce** — Identify minimal reproduction steps
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+ 2. **Trace data flow** — Follow the value/control flow from input to error
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+ 3. **Isolate** — Narrow to the smallest failing unit
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+ 4. **Hypothesize** — Form explicit hypothesis before reading more code
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+ 5. **Confirm** — Verify hypothesis against source, not just symptoms
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+
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+ Common root cause categories:
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+ - **Null/undefined** — missing guard, wrong assumption about data shape
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+ - **Race condition** — async ordering, missing await, shared mutable state
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+ - **External dependency** — timeout, API contract change, env difference
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+ - **Type mismatch** — serialization, casting, implicit coercion
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+ - **Configuration** — env var missing, wrong default, deployment drift
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+
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+ ---
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+
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+ ## Phase 4 — Log Analysis
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+
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+ 1. Read the full log output (not just the last line)
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+ 2. Identify: timestamps, error levels, request IDs, correlation tokens
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+ 3. Correlate events across log lines to build timeline
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+ 4. Look for: first occurrence, frequency, affected subset, preceding events
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+ 5. Summarize: what happened, when, why, and what was affected
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+
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+ ---
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+
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+ ## Phase 5 — Performance Profiling
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+
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+ 1. **Measure baseline** — Never optimize blind
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+ ```bash
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+ time <command>
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+ ```
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+ 2. **Profile** — Language-appropriate tools:
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+ - Node.js: `--prof`, `clinic.js`, `0x`
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+ - Python: `cProfile`, `py-spy`, `line_profiler`
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+ - Go: `pprof`
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+ 3. **Identify hotspot** — Usually 1–2 functions account for >80% of time; use `gitnexus_context` to confirm call frequency
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+ 4. **Fix the bottleneck** — Minimal targeted change
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+ 5. **Verify** — Measure again, compare against baseline
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+
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+ ---
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+
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+ ## Phase 6 — Remediation
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+
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+ 1. **Fix** — Minimal change that addresses the confirmed root cause
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+ 2. **Verify** — Run the failing case to confirm fix
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+ 3. **Regression test** — Add a test that would have caught this bug
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+ 4. **Check blast radius** — `gitnexus_impact({target: "fixedSymbol", direction: "upstream"})`
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+ 5. **Pre-commit scope check** — `gitnexus_detect_changes({scope: "staged"})`
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+
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+ ---
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+
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+ ## Checklist
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+
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+ ```
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+ - [ ] Read full error / stack trace
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+ - [ ] Identify suspect symbol
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+ - [ ] gitnexus_detect_changes to check for regressions
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+ - [ ] gitnexus_query for error text or symptom
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+ - [ ] gitnexus_context on suspect (callers, callees, processes)
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+ - [ ] Trace execution flow via process resource
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+ - [ ] Read source files to confirm root cause
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+ - [ ] Form explicit hypothesis before fixing
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+ - [ ] Verify fix against failing reproduction
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+ - [ ] Add regression test
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+ - [ ] gitnexus_detect_changes() before committing
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+ ```
@@ -78,6 +78,33 @@ If changes cannot be classified safely, stop with `BLOCKED_DIRTY_UNCLASSIFIED_CH
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  ---
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+ ## Stage 2.5 — Scope Verification
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+
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+ Before committing or pushing, verify that branch changes match the expected scope of the session's closed issues. **Never skip this step** — unreviewed scope is the primary source of oversized or unintended PRs.
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+
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+ Run:
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+ ```bash
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+ git diff --stat origin/main..HEAD 2>/dev/null || git diff --stat $(git merge-base HEAD main)..HEAD
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+ ```
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+
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+ For each significantly changed symbol, check blast radius:
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+ ```bash
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+ npx gitnexus impact <symbol-name> # upstream dependants — what else breaks
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+ npx gitnexus impact <symbol-name> -d downstream # downstream dependencies
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+ ```
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+
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+ For Claude agents with MCP access, also run:
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+ ```
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+ gitnexus_detect_changes({scope: "compare", base_ref: "main"})
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+ ```
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+
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+ **Rules:**
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+ - Changes clearly tied to session issues → continue
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+ - Files unrelated to session issues → classify as overscoped (handle in Stage 3D)
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+ - `npx gitnexus impact` returns HIGH or CRITICAL risk on a changed symbol → **stop and report to user** before continuing
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+
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+ ---
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+
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  ## Stage 3 — Dry Run and Anomaly Detection
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  Run:
@@ -260,6 +287,7 @@ If linkage had to be inferred from commits rather than detected by `xt end`, say
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  The autonomous rule is simple:
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  - normalize the session
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+ - verify scope with gitnexus before committing
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  - dry-run
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  - auto-fix predictable anomalies
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  - rerun dry-run