scip-query 0.10.8 → 0.10.11

package/dist/queries/wrapper-candidates.js

@@ -1,2 +1,2 @@
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+import{a}from"../chunk-7IVSJJZU.js";import"../chunk-GRJY65YT.js";import"../chunk-LM5SHAN4.js";import"../chunk-PFOCOG57.js";import"../chunk-B75HZHUP.js";import"../chunk-5OST6GYB.js";import"../chunk-C5CTSJ6X.js";import"../chunk-BGBBVSH4.js";import"../chunk-RNM6LMCF.js";import"../chunk-JCLDUKT6.js";import"../chunk-KDFONWTW.js";import"../chunk-OLTESY4K.js";import"../chunk-TQ5W2H3S.js";import"../chunk-TK7O5ER5.js";import"../chunk-VUKC6F77.js";import"../chunk-P5RYBRIO.js";import"../chunk-OBGRLXWF.js";import"../chunk-2KHTSEIL.js";import"../chunk-JM72FNGA.js";import"../chunk-72KY2ZFO.js";import"../chunk-YZA6PPZL.js";import"../chunk-HF25DFSC.js";import"../chunk-DS6QEB3G.js";import"../chunk-XUGQU7PM.js";import"../chunk-A536TEU4.js";import"../chunk-64MNV6AB.js";import"../chunk-7S5E7KWT.js";export{a as wrapperCandidates};
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package/docs/COMMAND_REFERENCE.md

@@ -115,7 +115,7 @@ This syntax summary is generated from the CLI command descriptors. Keep workflow
 
 | Command | Description | Options |
 |---|---|---|
-| `bench` | Benchmark indexing and command runtimes for this repository | `--json`<br>`--cold-index`<br>`--include-heavy`<br>`--command <cmd>`<br>`--timeout-ms <n>` |
+| `bench` | Benchmark indexing and command runtimes for this repository | `--json`<br>`--cold-index`<br>`--include-heavy`<br>`--command <cmd>`<br>`--timeout-ms <n>`<br>`--progress`<br>`--profile`<br>`--profile-out <path>` |
 | `install-skills` | Install skills (scip-query, scip-query-setup, scip-adoption, scip-health-audit, scip-health-improve, scip-hyper-optimization, scip-api-impact, concrete-plan, scip-ai-cleanup, scip-debug, scip-explore, scip-triage-issue, scip-diagram, scip-debloat, scip-doc-reconcile, scip-directory-architecture, scip-maintainability, scip-react-maintainability, scip-vue-maintainability, scip-verify, scip-language-playbook) into Claude Code, Codex, and shared agent roots | - |
 | `setup-hooks` | Install or refresh project-local Codex and Claude Code lifecycle hooks | `--json` |
 | `check-deps` | Check whether scip-query and the detected language indexers are actually runnable | - |

package/docs/analyzer-inventory.md

@@ -164,3 +164,32 @@ This should pair with `react-large-component-pressure`, `vue-large-view-pressure
 ## 2026-06-23 Citation Refresh
 
 The maintainability-register completion slice rechecked the command and diff-gate guide references above. `src/runtime/commands/query-command-specs.ts` still owns the public query order, now also exporting `orderedQueryCommandDescriptors` so CLI registration can derive from that order. `src/queries/impact/diff-gate.ts` still owns `DIFF_GATE_CHECKS`; the slice only centralized finding emission through a local recorder and did not change the listed check family.
+
+## 2026-06-28 Diff-Gate Echo Follow-Up
+
+The diff-gate implementation still owns `DIFF_GATE_CHECKS` and the default
+diff-scoped check family in `src/queries/impact/diff-gate.ts`. The
+hyper-optimization follow-up only adds a callable-symbol prefilter before the
+echo check invokes similarity, so the command surface and check inventory
+described above are unchanged.
+
+## 2026-06-28 Health Drift Performance Follow-Up
+
+The `src/queries/health/health.ts` citation remains accurate. The
+hyper-optimization follow-up only skips advisory drift `pattern-deviation` rows
+for health and baseline paths that already hide those rows; health scoring,
+phase inventory, and public `drift` output are unchanged.
+
+## 2026-06-28 Diff-Gate Co-Change Follow-Up
+
+The `src/queries/impact/diff-gate.ts` citation remains accurate. Diff-gate
+still owns `DIFF_GATE_CHECKS`; the co-change partner check now compares against
+the raw git changed-path set so changed docs and config files count as present
+even when they are not indexed code files.
+
+## 2026-06-28 Focused Co-Change History Follow-Up
+
+The `src/queries/impact/diff-gate.ts` citation remains accurate after the
+focused co-change history optimization. Diff-gate still owns the check list and
+co-change partner gate; the latest change only narrows the git-history read for
+that gate to commits in the bounded analysis window that touched changed files.

package/docs/analyzer-validation-ledger.md

@@ -15,7 +15,7 @@ The ledger is anchored to the current tool surface, not memory.
 | Surface                   | Source                                                                                                                                                                                                                                                                                                       | Why it anchors the ledger                                                                     |
 | ------------------------- | ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ | --------------------------------------------------------------------------------------------- |
 | Repo-wide health analysis | `scip-query code health --json` reported `src/queries/health/health.ts:194`, where `health()` runs `runHealthAnalyses()` and `buildHealthReport()`.                                                                                                                                                          | Every repo-wide analyzer validation must eventually reconcile with health output and scoring. |
-| Change-time gate analysis | `scip-query code diffGate --json` reported `src/queries/impact/diff-gate.ts:94`, where `diffGate()` runs the default diff-scoped checks: `echo`, `incomplete-migration`, `co-change-partner`, `doc-reference`, `unused-params`, and `new-dead`. The baseline ratchet is explicit because it is repo-wide. | Every diff-only analyzer needs a separate validation path from repo-wide health.              |
+| Change-time gate analysis | `scip-query code diffGate --json` reported `src/queries/impact/diff-gate.ts:94`, where `diffGate()` runs the default diff-scoped checks: `echo`, `incomplete-migration`, `co-change-partner`, `doc-reference`, `unused-params`, and `new-dead`. The baseline ratchet is explicit because it is repo-wide.    | Every diff-only analyzer needs a separate validation path from repo-wide health.              |
 | Public command registry   | `scip-query trace queryCommandOrder --json` reported `src/runtime/commands/query-command-specs.ts:10`, where the public query command order starts. `scip-query code queryCommandDescriptor --json` reported `src/runtime/commands/query-command-specs.ts:94`, where command descriptors are resolved by id. | The ledger must not silently miss a public analyzer command.                                  |
 | Diff-gate check list      | `scip-query trace DIFF_GATE_CHECKS --json` reported `src/queries/impact/diff-gate.ts:27`, where the canonical diff-gate check list is exported.                                                                                                                                                              | The ledger must cover every change-time check that can block a diff.                          |
 
@@ -268,3 +268,34 @@ The maintainability-register completion slice rechecked the ledger's command-sur
 ## 2026-06-23 Current Sweep Citation Refresh
 
 The current maintainability sweep rechecked the `diff-gate.ts` citation again after doc-reference and baseline policy helpers moved into private query modules. The ledger remains accurate because `diffGate()` and `DIFF_GATE_CHECKS` still live in `src/queries/impact/diff-gate.ts`; the baseline policy body remains behind the same entry point, but the repo-wide baseline ratchet is explicit rather than part of default diff-gate execution.
+
+## 2026-06-28 Diff-Gate Echo Follow-Up
+
+The `diffGate()` citation remains accurate: default diff-gate execution still
+runs echo, incomplete migration, co-change partner, doc-reference,
+unused-params, and new-dead checks through `src/queries/impact/diff-gate.ts`.
+The performance follow-up only skips non-callable changed symbols before echo
+similarity scoring; baseline ratchet behavior and check configuration remain
+unchanged.
+
+## 2026-06-28 Health Drift Performance Follow-Up
+
+The `src/queries/health/health.ts` reference remains accurate after the health
+drift optimization. Health and the baseline ratchet now ask `drift()` to skip
+advisory `pattern-deviation` rows they already exclude from visible output and
+stable finding identities; the repo-wide health score contract is unchanged.
+
+## 2026-06-28 Diff-Gate Co-Change Follow-Up
+
+The `diffGate()` citation remains accurate. Default diff-gate still runs the
+same check family; the co-change partner check now uses the raw git changed
+paths when deciding whether a historical partner is already present in the
+diff.
+
+## 2026-06-28 Focused Co-Change History Follow-Up
+
+The `diffGate()` citation remains accurate after the focused co-change history
+optimization. Default diff-gate still runs the same check family; the
+co-change partner check now reads only changed-file commits from the same
+bounded git-history window instead of parsing the whole name-only history
+payload.

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "scip-query",
-  "version": "0.10.8",
+  "version": "0.10.11",
   "description": "Evidence and verification for AI coding agents: map code, reuse concepts, finish migrations, and gate diffs.",
   "type": "module",
   "main": "dist/index.js",

package/skills/scip-hyper-optimization/SKILL.md

@@ -1,9 +1,10 @@
 ---
 name: scip-hyper-optimization
-description: Run scientific performance optimization campaigns with scip-query evidence, command ledgers, and benchmark corpora. Use when the user asks to hyper optimize, make commands blazing fast, speed up a CLI/tool/app, benchmark regressions, or compare targeted tuning against radically different implementations.
+description: Run scientific performance optimization campaigns with scip-query evidence, hierarchical profiling, command ledgers, and benchmark corpora. Use when the user asks to hyper optimize, make commands blazing fast, speed up a CLI/tool/app, find bottlenecks, benchmark regressions, optimize cold or warm paths, or compare targeted tuning against radically different implementations.
 ---
 
 # SCIP Hyper Optimization
+
 Use this skill to make a command, workflow, service, page, or tool as fast as
 feasibly possible without changing its observable result. Hyper optimization is
 a bounded campaign that improves runtime, memory use, or computational cost
@@ -12,9 +13,16 @@ benchmark and unchanged output.
 
 A measurement harness is the repeatable set of commands, fixtures, corpora,
 environment notes, and result documents used to decide whether performance
-changed. A command ledger is the living document for one target: what it
-returns, what code runs, where time is spent, what was tried, and what evidence
-accepted or rejected each idea.
+changed. A run history is the durable time-series of those measurements: one
+record per run, command, subprocess, or profiled stage, with enough metadata to
+compare commits and draw charts later. A profile span is one named timed piece
+of work inside the target process, such as input loading, cache reads, database
+queries, graph traversal, rendering, or a child process. Hierarchical profiling
+is using coarse spans to find the dominant stage, then recursively splitting
+only that stage until the expensive operation is concrete enough to fix. A
+command ledger is the living document for one target: what it returns, what code
+runs, where time is spent, what was tried, and what evidence accepted or
+rejected each idea.
 
 ## Rules
 
@@ -23,22 +31,43 @@ accepted or rejected each idea.
    `call-graph`, `code`, `dataflow`, `complexity`, `diff-impact`, `diff-gate`.
 3. Capture representative inputs, required output behavior, and correctness
    checks before editing.
-4. Measure cold and warm paths when both matter; record exact commands, corpus,
-   elapsed time, repetitions, and outliers.
-5. Work both tracks: tune the current pipeline and evaluate radically different
+4. Record every benchmark in a machine-readable run history before and after
+   each optimization; Markdown summaries are secondary.
+5. Measure cold-index, cold-cache or evidence-fill, warm steady-state, and
+   repeated focused paths separately when they can diverge.
+6. Profile the target's internal chain before editing. A bare command duration
+   is enough to rank targets, not enough to choose a fix.
+7. Treat profiling as a search algorithm: place coarse spans first, split the
+   biggest span, and stop descending only when the slow operation is identifiable
+   as a specific repeated lookup, initialization, scan, traversal, subprocess,
+   serialization step, or wait.
+8. Attach counts to spans: files, rows, symbols, candidates, cache hits/misses,
+   subprocesses, bytes, edges, nodes, retries, and output rows. Time without
+   cardinality hides the cause.
+9. Work both tracks: tune the current pipeline and evaluate radically different
    algorithms or data models that preserve the same result.
-6. Keep only changes that improve real workloads without reducing accuracy,
-   diagnostics, safety checks, or supported inputs.
+10. Keep only changes that improve real workloads without reducing accuracy,
+    diagnostics, safety checks, or supported inputs.
+
+## Phase 0: Target And Measurement Harness
 
-## Phase 0: Measurement Harness
 If the target repository is not already a reliable scip-query workspace, invoke
 `scip-query-setup` first. Do not run setup-ci in this workflow.
 
-Create or update a benchmark note before code changes. Prefer the repo's
-existing convention; otherwise use
-`docs/benchmarks/YYYY-MM-DD-<target>-baseline.md`. Include target, machine/date
+Choose the optimization target explicitly. Use user-reported pain, production
+telemetry, benchmark ranking, regression data, cost, frequency, or risk to
+justify why this target comes first. Do not optimize the slowest thing by habit
+if another path dominates real user time or compute spend.
+
+Create or update a benchmark note and a run-history store before code changes.
+Prefer the repo's existing convention; otherwise use
+`docs/benchmarks/YYYY-MM-DD-<target>-baseline.md` and
+`docs/benchmarks/runs/YYYY-MM-DD-<target>.jsonl`. Include target, machine/date
 context, corpus or fixture list, cold/warm/correctness commands, baseline
-timings, output-contract evidence, and slowest stages.
+timings, output-contract evidence, and slowest stages. Append a structured run
+record for each measurement with at least timestamp, commit/version, target,
+corpus, scenario, command, duration, exit status, output hash or size, and
+notes for outliers.
 
 Choose the measurement mechanism from the target's real workload. For app
 paths, use the app's benchmark, test, route smoke, build, profiler, load test,
@@ -51,13 +80,20 @@ scip-query bench --json
 scip-query bench --json --cold-index --include-heavy --timeout-ms 600000
 ```
 
+For long benchmark matrices, prefer progress output or incremental JSONL writes
+so the current command, subprocess, elapsed time, and completed measurements are
+visible while the run is still active and useful if interrupted.
+
 ## Phase 1: Command Ledger
+
 Create one ledger per target:
 `docs/benchmarks/YYYY-MM-DD-<target>-ledger.md`. Include Output Contract,
-Current Pipeline, Measurements, Current-Pipeline Optimizations, Alternative
-Designs, and Decisions.
+Target Selection, Current Pipeline, Run History Location, Profile Spans,
+Bottleneck Candidates, Measurements, Current-Pipeline Optimizations,
+Alternative Designs, and Decisions.
 
 ## Phase 2: Trace Current Behavior
+
 Trace the target end to end and write the actual path into the ledger:
 
 ```bash
@@ -72,26 +108,119 @@ scip-query complexity <hot-symbol>
 scip-query change-surface <touched-file> --json --full
 ```
 
-Record input parsing, lookups, database queries, graph traversal, source scans,
-semantic calls, cache reads/writes, rendering, and verification.
+Record the chain reaction from entry point to result: input parsing, option
+resolution, subprocesses, lookups, database queries, graph traversal, source
+scans, semantic calls, cache reads/writes, rendering, output serialization, and
+verification. The trace should be concrete enough that each major step can be
+timed as a profile span.
+
+Before adding spans, use the trace to predict span boundaries. Good first spans
+usually match the target's real pipeline nouns: load inputs, compute candidates,
+read cache, compute misses, write cache, build graph, score, render, serialize,
+and child process. Use `call-graph` to find nested helpers inside the slow
+stage, `dataflow` to follow the expensive object or cache key, `refs` to learn
+whether a suspected fix affects other paths, and `complexity` to avoid spending
+the first profiling pass on low-risk glue.
+
+## Phase 3: Profile The Timed Chain
+
+Before editing, produce a stage profile for the selected target. Prefer existing
+runtime profilers, tracing systems, structured logs, or benchmark hooks. If none
+exist, add temporary or permanent instrumentation that names timed spans without
+changing observable output. For CLIs and build tools, include child processes
+and worker tasks; for services, include request handlers, database calls,
+network calls, queue jobs, cache hits/misses, rendering, and serialization.
+
+Use this discovery ladder:
+
+1. Measure the target unprofiled so the user-facing baseline is real.
+2. Measure it profiled once. If profiled and unprofiled times are close, the
+   profiler is diagnostic overhead, not the bottleneck. If profiling dominates,
+   fix the harness before trusting fine spans.
+3. Measure distinct states separately: cold index, cold derived-cache/evidence
+   fill, warm cache hit, repeated focused run, and production-like mixed state.
+4. Add coarse spans that cover the whole chain. If span time does not explain
+   wall time, look for uninstrumented child processes, async waits, I/O, process
+   startup, or profiler gaps.
+5. Pick the largest span by wall time multiplied by real workload frequency.
+   Split only that span into child spans.
+6. Repeat until a fixable operation appears: a repeated singleton creation, a
+   per-item lookup, a broad scan, a wrapper traversal, a cache miss storm, a
+   subprocess startup, a serialization step, or a wait.
+7. Add cardinality metadata to every split: count of rows/files/symbols/nodes,
+   cache hits/misses, bytes, output rows, and skipped items.
+8. Record the before profile in the ledger before touching code.
+
+Write profile records to the run history with parent/child span names when
+possible. Separate wall time from CPU time when the tools allow it. Mark cache
+state explicitly: cold index, cold evidence/cache fill, warm cache hit, repeated
+focused run, or production-like mixed state.
+
+## Phase 4: Diagnose And Find Speedups
+
+Classify the dominant span before choosing a fix:
+
+| Profile shape                                         | Likely cause                                                                   | First fixes to test                                                                                               |
+| ----------------------------------------------------- | ------------------------------------------------------------------------------ | ----------------------------------------------------------------------------------------------------------------- |
+| Cold path huge, warm path fast                        | Derived evidence/cache fill, expensive initialization, or cache invalidation   | Persist the derived result, reuse compatible cache versions, batch cache fills, hoist initialization              |
+| Warm path still slow                                  | Cache scan, query shape, deserialization, reshaping, rendering, or output size | Narrow query, add indexes, store compact payloads, stream or avoid repeated object shaping                        |
+| Same expensive setup repeated across many files/items | Singleton/client/checker/session/project built inside a loop                   | Preload required inputs, create once after inputs are stable, cache per project/process                           |
+| Many medium-cost per-item operations                  | N+1 lookups, scalar provider calls, repeated source reads                      | Batch by provider/file/key, load rows in bulk, group work by locality                                             |
+| Traversal span grows with AST/source nodes            | Wrapper allocation or broad source scan                                        | Use lower-level APIs, prefilter by exact names only when output identity proves equivalence, index reusable facts |
+| Database time dominates                               | Broad scan, missing index, many statements, repeated prepares                  | Push filters into SQL, batch queries, cache prepared statements, add measured indexes                             |
+| Child process or startup dominates                    | Too many subprocesses or cold tool startup                                     | Reuse workers, batch commands, keep warm daemons, collapse process boundaries                                     |
+| Serialization/output dominates                        | Large JSON, repeated formatting, full materialization                          | Stream, summarize, avoid duplicate fields, or add an explicit compact mode                                        |
 
-## Phase 3: Find Speedups
 For the current pipeline, look for repeated work, broad scans, N+1 lookups,
 uncached pure work, avoidable source or semantic reads, large arrays, late
-filters, batchable per-file work, and safe parallelism.
+filters, batchable per-file work, excessive subprocess startup, serialization
+cost, cache invalidation churn, and safe parallelism. Prioritize by measured
+span cost multiplied by real workload frequency; do not chase a large cold-only
+span if the stated purpose depends on warm interactive latency.
+
+Favor fixes in this order when they preserve output:
+
+1. Remove accidental repetition: hoist, memoize, reuse, or preload.
+2. Batch scalar work by provider, file, database key, network endpoint, or
+   process.
+3. Move stable derived work from the hot path into an index/cache with a clear
+   invalidation key.
+4. Replace broad scans with indexed lookups or candidate-first retrieval.
+5. Replace high-overhead wrapper APIs with lower-level APIs only after output
+   identity checks prove equivalence.
+6. Add pruning only when it is mathematically equivalent or output-identity
+   checks across representative corpora prove no observable change.
 
 For alternative designs, restate the output contract first. Ask whether SQLite
 can answer directly, an index/cache/precomputed table can move work out of the
 hot path, batch queries can replace loops, a cheap pruning stage can precede
 exact work, or workers can run independent phases safely.
 
-## Phase 4: Implement and Verify
+## Phase 5: Implement And Verify
+
 Make the smallest reversible change that tests one performance hypothesis.
-Update the ledger with hypothesis, changed files/symbols, before/after timings,
-output comparison, tests, and gates.
+Update the ledger and run history with hypothesis, changed files/symbols,
+before/after timings, profile-span deltas, output comparison, tests, and gates.
+
+After each candidate fix, run the smallest valid before/after matrix for the
+target scenario: unprofiled control, profiled profile, output hash or semantic
+identity check, and representative correctness tests. If a faster change alters
+the output contract, reject or revert it unless the user explicitly approved a
+behavior change.
 
 Run the narrow correctness check, benchmark cases, `scip-query diff-impact
 --json`, and `scip-query diff-gate --json`; reindex first if freshness is not
 proven. Also run postchecks matching the change type. End with starting time,
 final time, percentage change, accepted changes, rejected ideas, remaining
-bottlenecks, and the next target.
+bottlenecks, and the next target. If results conflict, keep the change only when
+the target scenario and output contract justify it; otherwise revert and record
+the rejected hypothesis.
+
+## Phase 6: Report And Visualize
+
+End every optimization round with a compact scoreboard generated from the run
+history, not hand-copied memory. At minimum, show starting value, current value,
+delta, scenario, corpus, commit/version, and output identity evidence. When the
+history has enough rows, produce a trend table or chart for the target command
+or workflow. Keep Markdown readable for humans, but treat the structured
+history as the source of truth.

package/skills/scip-hyper-optimization/agents/openai.yaml

@@ -1,4 +1,4 @@
 interface:
-  display_name: "SCIP Hyper Optimization"
-  short_description: "Scientific benchmark-driven optimization"
-  default_prompt: "Use $scip-hyper-optimization to set up objective benchmarks, trace the target end to end, and optimize it without changing output."
+  display_name: 'SCIP Hyper Optimization'
+  short_description: 'Hierarchical profiling-driven optimization'
+  default_prompt: 'Use $scip-hyper-optimization to choose an optimization target, capture output identity, measure cold and warm controls, profile the dominant span hierarchically, then optimize without changing behavior.'

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package/dist/chunk-4TMJDHC6.js

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package/dist/chunk-5GVOJOBL.js

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package/dist/chunk-7XWXGANX.js

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-      );
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