scip-query 0.12.0 → 0.14.0

package/skills/_shared/SKILL.md

@@ -120,6 +120,9 @@ scip-query redundant-reexports # Find barrel re-exports that nobody imports thro
 scip-query duplicate-bodies # Find exact duplicate small-body candidates across files
 scip-query twin-drift # Twin drift candidates: same-name (or near-name) functions across files with diverged bodies
 scip-query twin-ab <symbolA> <symbolB> # Generate a behavioral A/B scaffold comparing two same-concept twins (scip-integrity-audit drill 5) — a ready-to-fill vitest file, not an auto-executor
+scip-query not-implemented # Reachable placeholder stub candidates (throw-stub, TODO+return-default, empty body) — production callers can actually reach these; an unreachable stub is dead's job, not this one's
+scip-query decorative-checkers # Decorative checker candidates: validate*/verify*/check*/assert*/is*/has* callables with no reachable failure exit anywhere in their body
+scip-query test-quality # Test-quality candidates: assertion-free it/test bodies, a skipped-test ledger with git-blame age, and mock-echo tests that assert the same literal they stubbed into a mock
 scip-query similar-signatures # Find functions with near-identical type signatures (same shape)
 ```
 
@@ -171,7 +174,7 @@ scip-query complexity <symbol> # Per-symbol complexity: branches, cyclomatic est
 
 ```bash
 scip-query bench # Benchmark indexing and command runtimes for this repository
-scip-query install-skills # Install skills (_shared, scip-query, scip-setup, scip-cleanup-audit, scip-cleanup-improve, scip-integrity-audit, scip-twin-drift, scip-claim-audit, scip-probe-reachability, scip-hyper-optimization, scip-api-impact, scip-concrete-plan, scip-conductor, scip-debug, scip-explore, scip-triage-issue, scip-diagram, scip-doc-reconcile, scip-directory-architecture, scip-maintainability, scip-react-maintainability, scip-vue-maintainability, scip-verify, scip-language-playbook, scip-tla-model-system) into Claude Code, Codex, and shared agent roots
+scip-query install-skills # Install skills (_shared, scip-query, scip-setup, scip-calibrate, scip-cleanup-audit, scip-cleanup-improve, scip-integrity-audit, scip-twin-drift, scip-claim-audit, scip-probe-reachability, scip-hyper-optimization, scip-api-impact, scip-concrete-plan, scip-conductor, scip-debug, scip-explore, scip-triage-issue, scip-diagram, scip-doc-reconcile, scip-directory-architecture, scip-maintainability, scip-react-maintainability, scip-vue-maintainability, scip-verify, scip-language-playbook, scip-tla-model-system) into Claude Code, Codex, and shared agent roots
 scip-query setup-hooks # Install or refresh project-local Codex and Claude Code lifecycle hooks
 scip-query check-deps # Check whether scip-query and the detected language indexers are actually runnable
 scip-query capabilities # Report which evidence and verification capabilities are available in this project

package/skills/scip-calibrate/SKILL.md

@@ -0,0 +1,124 @@
+---
+name: scip-calibrate
+description: Calibrate scip-query's detectors against a repo before trusting them. Use when adopting scip-query in a new or foreign codebase, after major detector changes, when a health score or gate output seems too noisy or too clean, or before letting diff-gate block anyone's work.
+commands:
+  - scip-query health --json
+  - scip-query diff-gate --base <commit> --json
+  - scip-query twin-drift -s <scope> --json
+  - scip-query dead --json
+  - scip-query similar <symbol>
+  - scip-query config-validate
+---
+
+# scip-calibrate
+
+Use this skill to measure whether scip-query's detectors tell the truth about a
+specific repository before believing anything they say about it. A detector
+tuned on one codebase's conventions can be precise there and noisy elsewhere;
+calibration is how you find out which you have — and it converts every noise
+archetype you find into either a repo-side knob or an upstream detector bug.
+
+Load shared mechanics from [`../_shared/SKILL.md`](../_shared/SKILL.md).
+
+## The Stance
+
+A health score you have not calibrated is a number, not a fact. Never present
+detector output from an uncalibrated repo as findings — present it as
+candidate findings pending classification. The score must EARN trust the same
+way a checker earns it in `scip-integrity-audit`: by being witnessed telling
+the truth on samples you verified yourself.
+
+## Protocol
+
+Run all five stages. Each has a checkable exit.
+
+### 1. Index and inventory
+
+`scip-query reindex`, then `scip-query status --capabilities`. Record which
+languages got which evidence tier (SCIP-indexed vs source-fallback vs regex) —
+a detector's expected precision differs per tier, and a repo that is 80%
+fallback-tier must be judged against fallback expectations. Note monorepo
+shape (workspaces, cross-package imports): historically the single largest
+false-positive source (dead/new-dead on cross-package consumers).
+Complete when: languages, tiers, and workspace shape are written down.
+
+### 2. Battery sweep
+
+Run the full detector battery and `health --json`. Do not react to anything
+yet — big numbers are not findings, they are sampling frames.
+Complete when: every detector's finding count is recorded.
+
+### 3. Retro-gate replay
+
+Replay `diff-gate` against the last 15–20 real commits (worktree per commit,
+never the user's live tree). This is the stage that exposes finding WALLS —
+one hub file or one convention mismatch generating dozens of near-identical
+findings per commit. A wall is always either a missing repo knob or a detector
+bug; it is never "the repo is just bad."
+Complete when: per-commit finding counts and every wall are recorded.
+
+### 4. Sample and classify — the actual calibration
+
+For each detector with findings: sample about 10 (all of them if fewer),
+READ THE CODE at each site, and classify actionable vs noise. Two rules make
+this real calibration instead of theater:
+
+- Classify from the code, never from the finding text. A finding that sounds
+  plausible and a finding that is true are different things; the difference is
+  only visible at the cited file and line.
+- For every noise finding, name the ARCHETYPE (e.g. "type-only import
+  invisible to indexer", "delegation chain flagged as twin", "generic shared
+  helpers saturating similarity"). Archetypes are the deliverable: a noise
+  rate without archetypes cannot be fixed.
+
+Then give each detector a verdict: **keep** (precision acceptable), **retune**
+(name the threshold and the value), or **demote to advisory** for this repo.
+Complete when: every detector has sampled precision, named archetypes, and a
+verdict.
+
+### 5. Tune the knobs, file the bugs
+
+Apply repo-side fixes for what belongs to the repo, and file upstream for what
+belongs to the detector:
+
+- `.scipquery.json` suppressions — one per accepted finding, WITH a reason;
+  a reasonless suppression is hiding, not tuning.
+- `docs.snapshotPaths` — dated/archival docs that must never generate
+  doc-reference findings.
+- Coverage contracts — enumerations the gate should police.
+- `commandAnalysisBudget` — cap analysis honestly on very large indexes.
+- Detector bugs (noise archetypes no knob can express) go to the tool's
+  followup ledger with the archetype, a concrete example, and the sampled
+  rate. Never tune a threshold to hide an archetype — that trades visible
+  noise for invisible blindness.
+
+Complete when: the gate replay from stage 3 re-runs materially quieter, and
+every remaining finding class is either actionable, suppressed-with-reason, or
+filed upstream.
+
+## Failure Modes (each observed in a real calibration)
+
+- **Sampling too few.** One good finding does not make a detector precise;
+  one bad finding does not make it noise. Ten per detector is the floor.
+- **Classifying from the finding text.** The finding always sounds right —
+  it was generated to. Only the code knows.
+- **Tuning to green.** Raising a threshold until the noise disappears also
+  disappears the real findings. If the archetype is a detector bug, file it
+  and live with the noise until it is fixed.
+- **Trusting a clean run.** Zero findings on a detector can mean precision or
+  can mean the detector cannot see this repo's conventions at all (wrong
+  import style, unindexed language). Verify at least one known-true positive
+  per major detector — plant one if none exists.
+- **Calibrating the wrong tree.** Clones or worktrees for anything that
+  mutates; the target repo is read-only unless its owner said otherwise.
+
+## After Calibration
+
+The finding-outcome ledger keeps calibrating for you: once the repo uses
+diff-gate, per-detector precision is recomputed from real outcomes
+(`detectorPrecision` in `health --json`). Re-run this protocol only after
+major detector upgrades or when the ledger's precision numbers drift from
+what you measured. Write the calibration report to
+`docs/validation/YYYY-MM-DD-external-calibration-<repo>.md` in the shape of
+the exemplars this skill was distilled from — battery table, retro-gate
+walls, per-detector verdicts, noise archetypes, caps and deviations.

package/skills/scip-calibrate/agents/openai.yaml

@@ -0,0 +1,4 @@
+interface:
+  display_name: "scip calibrate"
+  short_description: "Measure scip-query's detector precision on a repo before trusting scores or gating anyone."
+  default_prompt: "Run the scip-calibrate protocol against this repository: battery sweep, retro-gate replay, sample-and-classify each detector from the code, then tune repo knobs and file detector bugs."

package/skills/scip-integrity-audit/SKILL.md

@@ -9,6 +9,9 @@ commands:
   - scip-query twin-drift -s <scope> --json
   - scip-query twin-ab <symbolA> <symbolB>
   - scip-query outline <file> --signatures
+  - scip-query decorative-checkers -s <scope> --json
+  - scip-query not-implemented -s <scope> --json
+  - scip-query test-quality -s <scope> --json
 ---
 
 # scip-integrity-audit
@@ -43,6 +46,13 @@ decorative: file it as a defect, not a note.
 Complete only when every checker in scope has been witnessed rejecting a
 constructed should-fail input, or is listed with a reason it cannot be.
 
+Mechanized by: `scip-query decorative-checkers` finds `validate*`/`verify*`/
+`check*`/`assert*`/`is*`/`has*` callables with no reachable failure exit
+anywhere in their body (calibrated 2026-07-03 against two external repos —
+standalone-only; noise archetypes past one-hop delegation in
+`docs/validation/2026-07-03-integrity-detector-calibration.md`). Run it first
+to shortlist candidates before hand-constructing should-fail inputs.
+
 ### 2. Diff every adapter against captured reality
 
 For each parser/adapter of an external format (tool output, XML/JSON
@@ -65,6 +75,15 @@ feature above it is dead — date of death: birth.
 Complete only when every fallback's primary path has a witness or a filed
 defect.
 
+Mechanized by: `scip-query not-implemented` finds reachable placeholder
+stubs (`throw new Error('not implemented')`, TODO-comment + return-default,
+empty bodies) that a real caller, entry surface, or package-surface export
+can actually reach — the graph fact that separates "primary path never
+built" from `dead`'s "primary path built but unreferenced." Standalone-only
+(calibrated 2026-07-03; 0 live findings on two external repos post-fix, see
+the calibration report) — treat a clean run as "nothing this shape found,"
+not as "every fallback's primary path is proven live."
+
 ### 4. Hand-compute every metric twice
 
 For each number the system reports (scores, counts, estimates): pick two
@@ -101,3 +120,16 @@ the drill that exposed it, the should-fail input or real sample used, and
 the fix. The audit is complete only when every drill's exit criterion is
 met for the scope, and every defect found has a regression artifact — a
 test, fixture, or model that fails on the pre-fix behavior.
+
+A regression artifact that doesn't actually assert anything, or asserts the
+same literal it stubbed into its own mock, is a fake witness — the same
+"reports success without doing the work" failure mode this skill hunts in
+production code, just relocated to the test suite. Run `scip-query
+test-quality -s <scope>` over the audit's own regression artifacts (and,
+periodically, over the suite at large) to catch this: assertion-free test
+bodies, a skipped-test ledger with git-blame age (a skip with no fix date
+attached is a claim nobody is checking), and mock-echo (a test that only
+proves its own stub). Standalone-only, mixed precision by sub-check
+(calibrated 2026-07-03): assertion-free and skipped are high-precision;
+mock-echo is intentionally low-precision (syntactic same-literal matching,
+not dataflow) — treat its output as a reviewed candidate list, not a verdict.

package/skills/scip-tla-model-system/SKILL.md

@@ -21,19 +21,17 @@ Use this skill when a TypeScript system needs a TLA+ model tied to code evidence
 Load shared mechanics from [`../_shared/SKILL.md`](../_shared/SKILL.md).
 
 <!-- BEGIN GENERATED SKILL COMMANDS -->
-
 ## Commands for this skill
 
-| Command                                            | Purpose                                                                                                                                                                                  | When                                                                                    |
-| -------------------------------------------------- | ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- | --------------------------------------------------------------------------------------- |
-| `scip-query tla scaffold <file>`                   | TLA+ model workflow: verify a model and mapping contract, scaffold a draft model from indexed code, generate a trace recorder, or check a recorded trace against the next-state relation | Start here for a new model: derive a draft spec, config, and mapping from indexed code. |
-| `scip-query tla verify <spec>`                     | TLA+ model workflow: verify a model and mapping contract, scaffold a draft model from indexed code, generate a trace recorder, or check a recorded trace against the next-state relation | Mechanical conformance: referents, reads/writes, calls, and the model checker.          |
-| `scip-query tla instrument <spec>`                 | TLA+ model workflow: verify a model and mapping contract, scaffold a draft model from indexed code, generate a trace recorder, or check a recorded trace against the next-state relation | Generate a trace recorder plus wiring sites for each mapped action.                     |
-| `scip-query tla trace-check <spec> --trace <file>` | TLA+ model workflow: verify a model and mapping contract, scaffold a draft model from indexed code, generate a trace recorder, or check a recorded trace against the next-state relation | Semantic conformance: check a recorded execution against the model's Next relation.     |
-| `scip-query tla fetch-tools`                       | TLA+ model workflow: verify a model and mapping contract, scaffold a draft model from indexed code, generate a trace recorder, or check a recorded trace against the next-state relation | Download the pinned tla2tools.jar into the cache when the checker is unavailable.       |
+| Command | Purpose | When |
+| --- | --- | --- |
+| `scip-query tla scaffold <file>` | TLA+ model workflow: verify a model and mapping contract, scaffold a draft model from indexed code, generate a trace recorder, or check a recorded trace against the next-state relation | Start here for a new model: derive a draft spec, config, and mapping from indexed code. |
+| `scip-query tla verify <spec>` | TLA+ model workflow: verify a model and mapping contract, scaffold a draft model from indexed code, generate a trace recorder, or check a recorded trace against the next-state relation | Mechanical conformance: referents, reads/writes, calls, and the model checker. |
+| `scip-query tla instrument <spec>` | TLA+ model workflow: verify a model and mapping contract, scaffold a draft model from indexed code, generate a trace recorder, or check a recorded trace against the next-state relation | Generate a trace recorder plus wiring sites for each mapped action. |
+| `scip-query tla trace-check <spec> --trace <file>` | TLA+ model workflow: verify a model and mapping contract, scaffold a draft model from indexed code, generate a trace recorder, or check a recorded trace against the next-state relation | Semantic conformance: check a recorded execution against the model's Next relation. |
+| `scip-query tla fetch-tools` | TLA+ model workflow: verify a model and mapping contract, scaffold a draft model from indexed code, generate a trace recorder, or check a recorded trace against the next-state relation | Download the pinned tla2tools.jar into the cache when the checker is unavailable. |
 
 Use this shortlist first. Open [`../_shared/SKILL.md`](../_shared/SKILL.md) only when it is insufficient.
-
 <!-- END GENERATED SKILL COMMANDS -->
 
 ## Choose the Slice

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