scip-query 0.10.10 → 0.10.12

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "scip-query",
-  "version": "0.10.10",
+  "version": "0.10.12",
   "description": "Evidence and verification for AI coding agents: map code, reuse concepts, finish migrations, and gate diffs.",
   "type": "module",
   "main": "dist/index.js",
@@ -14,6 +14,7 @@
     "docs/assets/**/*",
     "docs/*.md",
     "scripts/build-scip-windows.mjs",
+    "scripts/evidence-product-contract.mjs",
     "skills/**/SKILL.md",
     "skills/**/agents/*.yaml",
     "vendor/scip/**/*"
@@ -291,6 +292,7 @@
     "typecheck": "tsc --noEmit",
     "lint": "npm run format:check && eslint src tests tsup.config.ts",
     "build:scip-windows": "node scripts/build-scip-windows.mjs",
+    "bench:evidence-products": "node scripts/evidence-product-contract.mjs",
     "calibrate": "node scripts/accuracy-calibration.mjs",
     "docs:commands": "vite-node scripts/render-command-reference.ts --write",
     "prepublishOnly": "npm run build && npm run build:scip-windows",

package/scripts/evidence-product-contract.mjs

@@ -0,0 +1,197 @@
+#!/usr/bin/env node
+import { spawnSync } from 'node:child_process';
+import { createHash } from 'node:crypto';
+import { existsSync, mkdirSync, rmSync, statSync, appendFileSync } from 'node:fs';
+import { dirname, join, resolve } from 'node:path';
+import { performance } from 'node:perf_hooks';
+
+const DEFAULT_COMMANDS = [
+  ['dead', '--json'],
+  ['doc-drift', '--json'],
+  ['recent-duplicates', '--json'],
+  ['similar', '--json', '--full'],
+  ['health', '--json', '--full'],
+];
+
+const args = parseArgs(process.argv.slice(2));
+const projectRoot = process.cwd();
+const cliPath = resolve(projectRoot, 'dist/cli.js');
+const date = new Date().toISOString().slice(0, 10);
+const runHistoryPath = resolve(projectRoot, args.out ?? `docs/benchmarks/runs/${date}-evidence-products.jsonl`);
+const profilePath = resolve(
+  projectRoot,
+  args.profileOut ?? `docs/benchmarks/runs/${date}-evidence-products.profile.jsonl`,
+);
+const commands = args.commands.length > 0 ? args.commands : DEFAULT_COMMANDS;
+
+mkdirSync(dirname(runHistoryPath), { recursive: true });
+mkdirSync(dirname(profilePath), { recursive: true });
+
+const status = runCli(['status', '--json'], { profile: false });
+if (status.exitCode !== 0) {
+  process.stderr.write(status.stderr.toString());
+  process.exit(status.exitCode ?? 1);
+}
+
+const statusJson = JSON.parse(status.stdout.toString());
+const dbPath = statusJson.result?.dbPath;
+if (typeof dbPath !== 'string') {
+  throw new Error('status --json did not include result.dbPath');
+}
+
+const evidencePath = join(dirname(dbPath), 'evidence.db');
+if (!args.noClear) clearEvidence(evidencePath);
+
+const runId = new Date().toISOString();
+const records = [];
+for (let iteration = 1; iteration <= args.coldIterations; iteration += 1) {
+  for (const command of commands) {
+    records.push(recordCommand({ runId, phase: 'cold-fill', iteration, command, evidencePath }));
+  }
+}
+for (let iteration = 1; iteration <= args.warmIterations; iteration += 1) {
+  for (const command of commands) {
+    records.push(recordCommand({ runId, phase: 'warm-hit', iteration, command, evidencePath }));
+  }
+}
+
+const failed = records.filter((record) => record.exitCode !== 0 || record.signal || record.error);
+const summary = {
+  runId,
+  runHistoryPath,
+  profilePath,
+  evidencePath,
+  commands: commands.map((command) => command.join(' ')),
+  coldIterations: args.coldIterations,
+  warmIterations: args.warmIterations,
+  failed: failed.length,
+  records: records.map(
+    ({ phase, iteration, command, durationMs, exitCode, stdoutBytes, stderrBytes, evidenceBytes }) => ({
+      phase,
+      iteration,
+      command,
+      durationMs,
+      exitCode,
+      stdoutBytes,
+      stderrBytes,
+      evidenceBytes,
+    }),
+  ),
+};
+
+process.stdout.write(`${JSON.stringify(summary, null, 2)}\n`);
+if (failed.length > 0) process.exit(1);
+
+function recordCommand({ runId, phase, iteration, command, evidencePath }) {
+  const result = runCli(command, { profile: true });
+  const record = {
+    timestamp: new Date().toISOString(),
+    runId,
+    target: 'evidence-products',
+    phase,
+    iteration,
+    command: `scip-query ${command.join(' ')}`,
+    durationMs: result.durationMs,
+    exitCode: result.exitCode,
+    signal: result.signal,
+    error: result.error?.message,
+    stdoutBytes: result.stdout.length,
+    stderrBytes: result.stderr.length,
+    stdoutSha256: sha256(result.stdout),
+    evidenceBytes: fileSize(evidencePath),
+    profilePath,
+  };
+  appendFileSync(runHistoryPath, `${JSON.stringify(record)}\n`);
+  return record;
+}
+
+function runCli(command, opts) {
+  const started = performance.now();
+  const result = spawnSync(process.execPath, [cliPath, ...command], {
+    cwd: projectRoot,
+    env: opts.profile
+      ? {
+          ...process.env,
+          SCIP_QUERY_PROFILE: '1',
+          SCIP_QUERY_PROFILE_COMMAND: `scip-query ${command.join(' ')}`,
+          SCIP_QUERY_PROFILE_OUT: profilePath,
+        }
+      : process.env,
+    encoding: 'buffer',
+    maxBuffer: 100 * 1024 * 1024,
+  });
+  return {
+    durationMs: Math.round(performance.now() - started),
+    exitCode: result.status,
+    signal: result.signal,
+    error: result.error,
+    stdout: result.stdout ?? Buffer.alloc(0),
+    stderr: result.stderr ?? Buffer.alloc(0),
+  };
+}
+
+function clearEvidence(evidencePath) {
+  for (const path of [evidencePath, `${evidencePath}-wal`, `${evidencePath}-shm`]) {
+    if (existsSync(path)) rmSync(path, { force: true });
+  }
+}
+
+function fileSize(path) {
+  try {
+    return statSync(path).size;
+  } catch {
+    return 0;
+  }
+}
+
+function sha256(buffer) {
+  return createHash('sha256').update(buffer).digest('hex');
+}
+
+function parseArgs(argv) {
+  const parsed = {
+    coldIterations: 1,
+    warmIterations: 2,
+    commands: [],
+    noClear: false,
+    out: undefined,
+    profileOut: undefined,
+  };
+  for (let index = 0; index < argv.length; index += 1) {
+    const arg = argv[index];
+    if (arg === '--cold-iterations') {
+      parsed.coldIterations = positiveInteger(argv[++index], '--cold-iterations');
+    } else if (arg === '--warm-iterations') {
+      parsed.warmIterations = positiveInteger(argv[++index], '--warm-iterations');
+    } else if (arg === '--command') {
+      const value = argv[++index];
+      if (!value) throw new Error('--command requires a value');
+      parsed.commands.push(splitCommand(value));
+    } else if (arg === '--out') {
+      parsed.out = argv[++index];
+      if (!parsed.out) throw new Error('--out requires a value');
+    } else if (arg === '--profile-out') {
+      parsed.profileOut = argv[++index];
+      if (!parsed.profileOut) throw new Error('--profile-out requires a value');
+    } else if (arg === '--no-clear') {
+      parsed.noClear = true;
+    } else {
+      throw new Error(`unknown option: ${arg}`);
+    }
+  }
+  return parsed;
+}
+
+function positiveInteger(value, flag) {
+  const parsed = Number(value);
+  if (!Number.isInteger(parsed) || parsed < 0) throw new Error(`${flag} must be a non-negative integer`);
+  return parsed;
+}
+
+function splitCommand(value) {
+  return value
+    .trim()
+    .split(/\s+/)
+    .filter(Boolean)
+    .filter((part, index) => !(index === 0 && part === 'scip-query'));
+}

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.'

package/dist/chunk-2UYQLFVC.js

@@ -1,2 +0,0 @@
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-//# sourceMappingURL=chunk-2UYQLFVC.js.map

package/dist/chunk-2VM46FC5.js

@@ -1,8 +0,0 @@
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package/dist/chunk-3Q77KKEY.js

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i=n.getSourceFile(),o=S(this.db.config.projectRoot,i.getFilePath());if(!o||this.db.isIgnored(o))continue;let s=y(i,n),a=H(this.db,o,s,e.getName());if(a)return{symbol:a.symbol,file:a.relativePath,line:a.startLine}}return null}calleeMapForFile(e){let t=this.sourceFiles.sourceFile(e);if(!t)return new Map;let n=g(this.db,e).sort((o,s)=>o.startLine-s.startLine||s.endLine-o.endLine);if(n.length===0)return new Map;let i=new Map;t.forEachDescendant(o=>{if(!this.tsMorph.Node.isCallExpression(o)&&!this.tsMorph.Node.isNewExpression(o))return;let s=this.semanticCalleeForCallNode(t,n,o);s&&je(i,s.callerId,s.target)});for(let[o,s]of i)i.set(o,Ae(s));return i}semanticCalleeForCallNode(e,t,n){let i=we(t,y(e,n));if(!i)return null;let o=n.getExpression(),s=o.getSymbol()??o.getType().getSymbol(),a=s?this.definitionFromSymbol(s):null;return a?{callerId:i.symbolId,target:{symbol:a.symbol,file:a.file,line:a.line}}:null}};function le(r){let e=[],t=r.getDefaultImport();t&&e.push({identifier:t,importedName:"default",localName:t.getText(),kind:"default",isTypeOnly:r.getImportClause()?.isTypeOnly()??!1});let n=r.getNamespaceImport();n&&e.push({identifier:n,importedName:"*",localName:n.getText(),kind:"namespace",isTypeOnly:r.getImportClause()?.isTypeOnly()??!1});for(let i of r.getNamedImports()){let o=i.getNameNode(),a=i.getAliasNode()??(o.getKindName()==="Identifier"?o:null);e.push({identifier:a,importedName:o.getText(),localName:a?.getText()??o.getText(),kind:"named",isTypeOnly:i.isTypeOnly()||(r.getImportClause()?.isTypeOnly()??!1)})}return e.length===0&&e.push({identifier:null,importedName:"*",localName:null,kind:"side-effect",isTypeOnly:!1}),e}function Ee(r,e,t){return{importer:r,sourcePath:e,importedName:t.importedName,localName:t.localName,kind:t.kind,isTypeOnly:!0,isUsed:!0,isTypeUsed:!0,isValueUsed:!1,references:[]}}function je(r,e,t){let n=r.get(e);n||(n=[],r.set(e,n)),n.push(t)}function we(r,e){let t=null;for(let n 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