@fairfox/polly 0.80.0 → 0.81.0

package/dist/tools/mutate/src/cli.js.map

@@ -0,0 +1,19 @@
+{
+  "version": 3,
+  "sources": ["../tools/mutate/src/args.ts", "../tools/mutate/src/config.ts", "../tools/test/src/coverage-policy/mutate-targets.ts", "../tools/mutate/src/decisions.ts", "../tools/mutate/src/ingest.ts", "../tools/mutate/src/init.ts", "../tools/mutate/src/run.ts", "../tools/mutate/src/report.ts", "../tools/mutate/src/verify-matrix.ts", "../tools/mutate/src/cli.ts"],
+  "sourcesContent": [
+    "/**\n * Argument parsing for `polly mutate`. Hand-rolled (matching the rest of the\n * polly CLI), with the value-flag / bool-flag split that lets a flag value\n * (`--report path.json`) not be mistaken for a positional verb.\n */\n\nexport interface MutateArgs {\n  /** First positional: \"run\" (default when bare) | \"report\" | \"decisions\" | \"verify\" | an unknown token to error on. */\n  verb: string;\n  /** Positionals after the verb (e.g. [\"decide\", file, verdict, ...rationale] for `decisions decide …`). */\n  rest: string[];\n  config?: string;\n  report?: string;\n  decisions?: string;\n  db?: string;\n  noReport: boolean;\n  /** `verify --run` (run a fresh Stryker pass before checking the contract). */\n  run: boolean;\n  /** `init --force` (overwrite an existing stryker.conf.json). */\n  force: boolean;\n  help: boolean;\n}\n\nconst KNOWN_VERBS = new Set([\"run\", \"report\", \"decisions\", \"verify\", \"init\", \"help\"]);\nconst VALUE_FLAGS = new Set([\"--config\", \"--report\", \"--decisions\", \"--db\"]);\n\nexport function parseMutateArgs(argv: string[]): MutateArgs {\n  const positionals: string[] = [];\n  const flags = new Map<string, string>();\n  const bools = new Set<string>();\n\n  let i = 0;\n  while (i < argv.length) {\n    const a = argv[i];\n    if (a === undefined) break;\n    if (VALUE_FLAGS.has(a)) {\n      flags.set(a, argv[i + 1] ?? \"\");\n      i += 2;\n    } else {\n      if (a.startsWith(\"-\")) bools.add(a);\n      else positionals.push(a);\n      i += 1;\n    }\n  }\n\n  const verbRaw = positionals[0];\n  const help = bools.has(\"--help\") || bools.has(\"-h\") || verbRaw === \"help\";\n  const verb = verbRaw === undefined ? \"run\" : KNOWN_VERBS.has(verbRaw) ? verbRaw : verbRaw;\n\n  return {\n    verb,\n    rest: positionals.slice(1),\n    config: flags.get(\"--config\"),\n    report: flags.get(\"--report\"),\n    decisions: flags.get(\"--decisions\"),\n    db: flags.get(\"--db\"),\n    noReport: bools.has(\"--no-report\"),\n    run: bools.has(\"--run\"),\n    force: bools.has(\"--force\"),\n    help,\n  };\n}\n",
+    "/**\n * Resolve the paths and Stryker config `polly mutate` works with. Everything is\n * resolved against the cwd the command was invoked from, so a consumer's project\n * tree works the same as this repo. Stryker-config discovery reuses the existing\n * `findStrykerConfigs` helper that `polly coverage` already depends on.\n */\nimport { resolve } from \"node:path\";\nimport { findStrykerConfigs } from \"../../test/src/coverage-policy/mutate-targets.ts\";\nimport type { MutateArgs } from \"./args.ts\";\n\nconst DEFAULT_REPORT = \"reports/mutation/mutation.json\";\nconst DEFAULT_DECISIONS = \".polly/test-debt/decisions.jsonl\";\n\nexport interface MutateConfig {\n  cwd: string;\n  /** The Stryker config to use — explicit `--config`, else the first discovered. Null if none found. */\n  strykerConfigPath: string | null;\n  /** mutation-testing-report-schema JSON the analysis reads. */\n  reportPath: string;\n  /** Intermediate SQLite db (\":memory:\" by default; a path persists it). */\n  dbPath: string;\n  /** Version-controlled human-verdict log. */\n  decisionsPath: string;\n}\n\nexport async function resolveMutateConfig(cwd: string, args: MutateArgs): Promise<MutateConfig> {\n  let strykerConfigPath: string | null = null;\n  if (args.config) {\n    strykerConfigPath = resolve(cwd, args.config);\n  } else {\n    // findStrykerConfigs returns sorted absolute paths; the root stryker.conf.json\n    // sorts before any stryker/ shard, so [0] is the root config when present.\n    const found = await findStrykerConfigs(cwd);\n    strykerConfigPath = found[0] ?? null;\n  }\n\n  return {\n    cwd,\n    strykerConfigPath,\n    reportPath: resolve(cwd, args.report ?? DEFAULT_REPORT),\n    dbPath: args.db ? resolve(cwd, args.db) : \":memory:\",\n    decisionsPath: resolve(cwd, args.decisions ?? DEFAULT_DECISIONS),\n  };\n}\n",
+    "/**\n * @fairfox/polly/test/coverage — Stryker mutate-/test-target validation.\n *\n * A Stryker config's `mutate` and `testFiles` lists are hand-curated. A path\n * that is renamed, or a glob whose directory moves, silently resolves to\n * nothing — Stryker mutates fewer files (or none) and the only signal is a\n * long mutation run whose score quietly drops. This asserts, in milliseconds,\n * that every entry still resolves to at least one file.\n *\n * Discovers configs two ways, covering both layouts in the wild: a single\n * `stryker.conf.json` at the root, and a `stryker/` directory of per-package\n * shards.\n */\n\nimport { existsSync, readFileSync } from \"node:fs\";\nimport { join, resolve } from \"node:path\";\nimport { Glob } from \"bun\";\n\ninterface StrykerConfig {\n  mutate?: string[];\n  testFiles?: string[];\n  bun?: { testFiles?: string[] };\n}\n\nexport interface MutateTargetIssue {\n  config: string;\n  field: \"mutate\" | \"testFiles\";\n  pattern: string;\n}\n\nexport interface MutateTargetReport {\n  configs: string[];\n  issues: MutateTargetIssue[];\n}\n\n/** Locate every Stryker config under the project root. */\nexport async function findStrykerConfigs(root: string): Promise<string[]> {\n  const found: string[] = [];\n  const single = join(root, \"stryker.conf.json\");\n  if (existsSync(single)) found.push(single);\n\n  const glob = new Glob(\"stryker/*.{json,conf.json}\");\n  for await (const rel of glob.scan({ cwd: root, onlyFiles: true })) {\n    found.push(join(root, rel));\n  }\n  return found.sort();\n}\n\nfunction isGlob(pattern: string): boolean {\n  return pattern.includes(\"*\") || pattern.includes(\"?\") || pattern.includes(\"[\");\n}\n\nasync function resolvesToFile(pattern: string, cwd: string): Promise<boolean> {\n  if (pattern.startsWith(\"!\")) return true; // negations are filters, not targets\n  if (!isGlob(pattern)) return existsSync(resolve(cwd, pattern));\n  const glob = new Glob(pattern);\n  for await (const _ of glob.scan({ cwd, onlyFiles: true })) return true;\n  return false;\n}\n\nasync function checkField(\n  configPath: string,\n  field: \"mutate\" | \"testFiles\",\n  patterns: string[] | undefined,\n  cwd: string\n): Promise<MutateTargetIssue[]> {\n  const issues: MutateTargetIssue[] = [];\n  for (const pattern of patterns ?? []) {\n    if (!(await resolvesToFile(pattern, cwd))) {\n      issues.push({ config: configPath, field, pattern });\n    }\n  }\n  return issues;\n}\n\n/**\n * Validate every Stryker config under `root`. Paths in a Stryker config are\n * relative to that config's directory; for the monorepo-root configs that is\n * the root, so we resolve globs against `root`.\n */\nexport async function validateMutateTargets(root: string): Promise<MutateTargetReport> {\n  const configs = await findStrykerConfigs(root);\n  const issues: MutateTargetIssue[] = [];\n  for (const configPath of configs) {\n    const config = JSON.parse(readFileSync(configPath, \"utf8\")) as unknown as StrykerConfig;\n    const testFiles = config.testFiles ?? config.bun?.testFiles;\n    issues.push(...(await checkField(configPath, \"mutate\", config.mutate, root)));\n    issues.push(...(await checkField(configPath, \"testFiles\", testFiles, root)));\n  }\n  return { configs, issues };\n}\n",
+    "/**\n * Decisions log — the version-controlled human-judgement layer.\n *\n * The signals (kill matrix, subsumption) are derived and regenerable; they live\n * in the gitignored SQLite db. *Decisions* about them — \"this subsumed file is a\n * legitimate set of input-class guards, keep it\" — are precious, can't be\n * regenerated, and are committed here as JSONL (one record per line: mergeable,\n * diffable, append-only, last-write-wins per file).\n *\n * Identity is the test FILE (stable across describe restructuring; git tracks\n * renames). Each decision stores two freshness stamps:\n *   - hash:   a normalised content hash of the test file at decision time.\n *             Differs → the test changed since you judged it → re-review.\n *   - signal: the subsumption snapshot at decision time. Drifts (e.g. a test\n *             elsewhere was deleted, so this file's kills became unique) → the\n *             matrix around it changed → re-review.\n *\n * A decision is trusted only while BOTH still hold. That's what stops a \"keep\"\n * verdict from silently outliving the reason it was made.\n *\n *   polly mutate decisions                          # status (the join)\n *   polly mutate decisions decide <file> <verdict> \"<rationale>\"\n *\n * verdicts: keep | prune | rewrite | investigate\n */\nimport type { Database } from \"bun:sqlite\";\nimport { createHash } from \"node:crypto\";\nimport { buildDb, loadMutationReport, queryAll } from \"./ingest.ts\";\n\nconst DEFAULT_LOG = \".polly/test-debt/decisions.jsonl\";\nconst DEFAULT_REPORT = \"reports/mutation/mutation.json\";\nconst VERDICTS = [\"keep\", \"prune\", \"rewrite\", \"investigate\"];\n\nexport interface FileSignal {\n  kills: number;\n  uniqueKills: number;\n  subsumed: boolean;\n}\ninterface Decision {\n  file: string;\n  verdict: string;\n  rationale: string;\n  signal: FileSignal;\n  hash: string | null;\n  decided: string;\n}\n\n/** Strip comments + collapse whitespace so formatting/comment edits don't trip the stamp.\n *  Heuristic (not a full parser): a false change only triggers a harmless re-review. */\nfunction normalizeSource(src: string): string {\n  return src\n    .replace(/\\/\\*[\\s\\S]*?\\*\\//g, \"\")\n    .replace(/(^|[^:])\\/\\/[^\\n]*/g, \"$1\")\n    .replace(/\\s+/g, \" \")\n    .trim();\n}\nasync function fileHash(file: string): Promise<string | null> {\n  const f = Bun.file(file);\n  if (!(await f.exists())) return null;\n  return createHash(\"sha256\")\n    .update(normalizeSource(await f.text()))\n    .digest(\"hex\")\n    .slice(0, 16);\n}\n\nexport function fileSignals(db: Database): Map<string, FileSignal> {\n  const rows = queryAll<{ file: string; kills: number; unique_kills: number }>(\n    db,\n    `\n\t\t\tWITH file_kill AS (SELECT DISTINCT t.file file, k.mutant_id mid FROM kills k JOIN tests t ON t.id=k.test_id),\n\t\t\t     owner AS (SELECT mid, count(DISTINCT file) nf FROM file_kill GROUP BY mid)\n\t\t\tSELECT fk.file file, count(DISTINCT fk.mid) kills,\n\t\t\t       sum(CASE WHEN o.nf=1 THEN 1 ELSE 0 END) unique_kills\n\t\t\tFROM file_kill fk JOIN owner o ON o.mid=fk.mid GROUP BY fk.file`\n  );\n  const m = new Map<string, FileSignal>();\n  for (const r of rows)\n    m.set(r.file, {\n      kills: r.kills,\n      uniqueKills: r.unique_kills,\n      subsumed: r.kills > 0 && r.unique_kills === 0,\n    });\n  return m;\n}\n\nasync function loadDecisions(logPath: string): Promise<Map<string, Decision>> {\n  const m = new Map<string, Decision>();\n  const f = Bun.file(logPath);\n  if (!(await f.exists())) return m;\n  for (const line of (await f.text()).split(\"\\n\")) {\n    const t = line.trim();\n    if (!t) continue;\n    const d = JSON.parse(t) as unknown as Decision;\n    m.set(d.file, d); // last write wins\n  }\n  return m;\n}\n\n/** Why a decision no longer applies, or null if it still holds. */\nfunction staleReason(\n  d: Decision,\n  currentHash: string | null,\n  current: FileSignal | undefined\n): string | null {\n  if (!current) return \"file no longer kills any mutant (renamed/deleted/refactored?)\";\n  if (d.hash !== currentHash) return \"test file changed since the decision\";\n  if (d.signal.subsumed !== current.subsumed)\n    return `subsumption flipped (${d.signal.subsumed} → ${current.subsumed})`;\n  if (d.signal.uniqueKills > 0 !== current.uniqueKills > 0)\n    return `unique-kill status changed (${d.signal.uniqueKills} → ${current.uniqueKills})`;\n  return null;\n}\n\n// biome-ignore lint/complexity/noExcessiveCognitiveComplexity: a linear join of signals against decisions — clearer as one pass than split.\nexport async function status(db: Database, logPath: string = DEFAULT_LOG): Promise<string> {\n  const signals = fileSignals(db);\n  const decisions = await loadDecisions(logPath);\n  const needsReview: string[] = [];\n  const stale: string[] = [];\n  const settled: string[] = [];\n\n  for (const [file, sig] of [...signals].sort((a, b) => b[1].kills - a[1].kills)) {\n    const d = decisions.get(file);\n    if (!d) {\n      if (sig.subsumed) needsReview.push(`  ${file}  (${sig.kills} kills, 0 unique)`);\n      continue;\n    }\n    const reason = staleReason(d, await fileHash(file), sig);\n    if (reason) stale.push(`  ${file}  [${d.verdict}] — ${reason}`);\n    else settled.push(`  ${file}  [${d.verdict}] ${d.rationale ? `— ${d.rationale}` : \"\"}`);\n  }\n  // decided files that have dropped out of the signal set entirely\n  for (const [file, d] of decisions) {\n    if (!signals.has(file)) stale.push(`  ${file}  [${d.verdict}] — file no longer in matrix`);\n  }\n\n  const out: string[] = [];\n  out.push(`NEEDS REVIEW  (subsumed files with no decision — ${needsReview.length})`);\n  out.push(needsReview.length ? needsReview.join(\"\\n\") : \"  none\");\n  out.push(`\\nSTALE  (decision's basis drifted — re-review — ${stale.length})`);\n  out.push(stale.length ? stale.join(\"\\n\") : \"  none\");\n  out.push(`\\nSETTLED  (fresh decisions, suppressed from action list — ${settled.length})`);\n  out.push(settled.length ? settled.join(\"\\n\") : \"  none\");\n  return out.join(\"\\n\");\n}\n\nexport async function decide(\n  file: string,\n  verdict: string,\n  rationale: string,\n  db: Database,\n  logPath: string = DEFAULT_LOG\n) {\n  if (!VERDICTS.includes(verdict)) {\n    console.log(`✗ verdict must be one of: ${VERDICTS.join(\", \")}`);\n    process.exit(1);\n  }\n  const sig = fileSignals(db).get(file);\n  if (!sig) {\n    console.log(`✗ ${file} is not a test file that kills any mutant in the current matrix`);\n    process.exit(1);\n  }\n  const decided = new Date().toISOString().slice(0, 10);\n  const record: Decision = {\n    file,\n    verdict,\n    rationale,\n    signal: sig,\n    hash: await fileHash(file),\n    decided,\n  };\n  await Bun.write(\n    logPath,\n    ((await Bun.file(logPath).exists()) ? await Bun.file(logPath).text() : \"\") +\n      JSON.stringify(record) +\n      \"\\n\"\n  );\n  console.log(`✓ recorded: ${file} [${verdict}]${rationale ? ` — ${rationale}` : \"\"}`);\n}\n\nif (import.meta.main) {\n  const db = buildDb(await loadMutationReport(DEFAULT_REPORT), \"reports/test-debt.sqlite\");\n  const [cmd, ...rest] = process.argv.slice(2);\n  if (cmd === \"decide\") {\n    const [file, verdict, ...r] = rest;\n    if (!file || !verdict) {\n      console.log('usage: decide <file> <keep|prune|rewrite|investigate> \"<rationale>\"');\n      process.exit(1);\n    }\n    await decide(file, verdict, r.join(\" \").replace(/^\"|\"$/g, \"\"), db);\n  } else {\n    console.log(await status(db));\n  }\n  db.close();\n}\n",
+    "/**\n * Ingest a Stryker mutation report (mutation-testing-report-schema) into a\n * regenerable SQLite database holding the kill matrix.\n *\n * The tool consumes the *schema*, never a specific runner — so the same\n * analysis works whether the matrix came from the patched bun runner, the\n * tap runner, or an eventual official Bun plugin. The db is a build artefact\n * (gitignored); decisions are kept elsewhere in version control.\n */\nimport { Database } from \"bun:sqlite\";\n\nexport interface MutationReport {\n  schemaVersion: string;\n  files: Record<string, { mutants: Mutant[] }>;\n  testFiles?: Record<string, { tests: TestDef[] }>;\n}\ninterface Mutant {\n  id: string;\n  mutatorName: string;\n  status: string;\n  location: { start: { line: number; column: number } };\n  killedBy?: string[];\n  coveredBy?: string[];\n}\ninterface TestDef {\n  id: string;\n  name: string;\n  location?: { start: { line: number; column: number } };\n}\n\nexport function buildDb(report: MutationReport, dbPath = \":memory:\"): Database {\n  const db = new Database(dbPath);\n  db.exec(\"PRAGMA journal_mode = WAL;\");\n  db.exec(`\n\t\tDROP TABLE IF EXISTS kills;\n\t\tDROP TABLE IF EXISTS covers;\n\t\tDROP TABLE IF EXISTS mutants;\n\t\tDROP TABLE IF EXISTS tests;\n\t\tCREATE TABLE tests (\n\t\t\tid TEXT PRIMARY KEY,\n\t\t\tfile TEXT NOT NULL,\n\t\t\tname TEXT NOT NULL,\n\t\t\tline INTEGER\n\t\t);\n\t\tCREATE TABLE mutants (\n\t\t\tid TEXT PRIMARY KEY,\n\t\t\tmutator TEXT NOT NULL,\n\t\t\tfile TEXT NOT NULL,\n\t\t\tline INTEGER,\n\t\t\tstatus TEXT NOT NULL\n\t\t);\n\t\t-- the kill matrix: (mutant, test) where test detects mutant\n\t\tCREATE TABLE kills (\n\t\t\tmutant_id TEXT NOT NULL REFERENCES mutants(id),\n\t\t\ttest_id TEXT NOT NULL REFERENCES tests(id),\n\t\t\tPRIMARY KEY (mutant_id, test_id)\n\t\t);\n\t\t-- coverage matrix (populated only when the runner reports coveredBy)\n\t\tCREATE TABLE covers (\n\t\t\tmutant_id TEXT NOT NULL REFERENCES mutants(id),\n\t\t\ttest_id TEXT NOT NULL REFERENCES tests(id),\n\t\t\tPRIMARY KEY (mutant_id, test_id)\n\t\t);\n\t\tCREATE INDEX idx_kills_test ON kills(test_id);\n\t\tCREATE INDEX idx_kills_mutant ON kills(mutant_id);\n\t`);\n\n  const insTest = db.prepare(\n    \"INSERT OR IGNORE INTO tests (id, file, name, line) VALUES (?, ?, ?, ?)\"\n  );\n  const insMut = db.prepare(\n    \"INSERT INTO mutants (id, mutator, file, line, status) VALUES (?, ?, ?, ?, ?)\"\n  );\n  const insKill = db.prepare(\"INSERT OR IGNORE INTO kills (mutant_id, test_id) VALUES (?, ?)\");\n  const insCover = db.prepare(\"INSERT OR IGNORE INTO covers (mutant_id, test_id) VALUES (?, ?)\");\n\n  // biome-ignore lint/complexity/noExcessiveCognitiveComplexity: two flat insert loops inside one transaction — keeping them together is the point.\n  const ingest = db.transaction(() => {\n    for (const [file, tf] of Object.entries(report.testFiles ?? {})) {\n      for (const t of tf.tests) {\n        insTest.run(t.id, file || \"(unknown)\", t.name, t.location?.start.line ?? null);\n      }\n    }\n    for (const [file, f] of Object.entries(report.files)) {\n      for (const m of f.mutants) {\n        insMut.run(m.id, m.mutatorName, file, m.location.start.line, m.status);\n        for (const tid of m.killedBy ?? []) insKill.run(m.id, tid);\n        for (const tid of m.coveredBy ?? []) insCover.run(m.id, tid);\n      }\n    }\n  });\n  ingest();\n  return db;\n}\n\n// SQL rows and the on-disk report arrive untyped; these three helpers are the\n// single sanctioned cast boundary (the `as unknown as` escape hatch) so call\n// sites stay assertion-free and the column/shape types live next to the query.\nexport function queryAll<T>(db: Database, sql: string): T[] {\n  return db.query(sql).all() as unknown as T[];\n}\nexport function queryGet<T>(db: Database, sql: string): T | null {\n  return db.query(sql).get() as unknown as T | null;\n}\nexport async function loadMutationReport(path: string): Promise<MutationReport> {\n  return (await Bun.file(path).json()) as unknown as MutationReport;\n}\n\nif (import.meta.main) {\n  const reportPath = process.argv[2] ?? \"reports/mutation/mutation.json\";\n  const dbPath = process.argv[3] ?? \"reports/test-debt.sqlite\";\n  const db = buildDb(await loadMutationReport(reportPath), dbPath);\n  const n = queryGet<{ t: number; m: number; k: number }>(\n    db,\n    \"SELECT (SELECT count(*) FROM tests) t, (SELECT count(*) FROM mutants) m, (SELECT count(*) FROM kills) k\"\n  ) ?? { t: 0, m: 0, k: 0 };\n  console.log(`Ingested ${reportPath} -> ${dbPath}`);\n  console.log(`  ${n.t} tests, ${n.m} mutants, ${n.k} kill-edges`);\n  db.close();\n}\n",
+    "/**\n * `polly mutate init` — scaffold a `stryker.conf.json` for a project that\n * depends on @fairfox/polly, wired with the verify-primitive ignorer preset.\n *\n * The one fiddly bit is the plugin reference. Stryker's plugin loader resolves\n * specifiers from inside its OWN package, so the bare \"@fairfox/polly/stryker\"\n * only resolves on a flat node_modules layout. In a workspace (monorepo) or a\n * Bun-isolated install it must be referenced by path to the built file. We\n * resolve the actual plugin via Bun's resolver and pick the form that will load.\n */\nimport { existsSync } from \"node:fs\";\nimport { join, relative } from \"node:path\";\n\nexport interface InitResult {\n  configPath: string;\n  /** false when a config already existed and --force was not passed. */\n  created: boolean;\n  pluginRef: string;\n  mutate: string[];\n  testGlob: string;\n  warnings: string[];\n}\n\n/**\n * The reference to write for the @fairfox/polly/stryker plugin: the bare\n * specifier when @fairfox/polly is hoisted into a flat node_modules (Stryker\n * resolves it), else a relative path to the built file (workspace / Bun-isolated).\n */\nfunction resolvePluginRef(projectDir: string): string {\n  const resolved = Bun.resolveSync(\"@fairfox/polly/stryker\", projectDir);\n  const hoisted = resolved.includes(\"/node_modules/\") && !resolved.includes(\"/.bun/\");\n  return hoisted ? \"@fairfox/polly/stryker\" : relative(projectDir, resolved);\n}\n\nfunction detectMutate(projectDir: string): string[] {\n  if (existsSync(join(projectDir, \"src\"))) {\n    return [\"src/**/*.ts\", \"!src/**/*.test.ts\", \"!src/**/*.d.ts\"];\n  }\n  return [\"**/*.ts\", \"!**/*.test.ts\", \"!**/*.d.ts\", \"!node_modules/**\", \"!dist/**\"];\n}\n\nfunction detectTestGlob(projectDir: string): string {\n  for (const d of [\"tests\", \"test\"]) {\n    if (existsSync(join(projectDir, d))) return `${d}/**/*.test.ts`;\n  }\n  return \"**/*.test.ts\";\n}\n\nexport async function initConfig(\n  projectDir: string,\n  opts: { force?: boolean } = {}\n): Promise<InitResult> {\n  const configPath = join(projectDir, \"stryker.conf.json\");\n  const warnings: string[] = [];\n\n  let pluginRef: string;\n  try {\n    pluginRef = resolvePluginRef(projectDir);\n  } catch {\n    throw new Error(\n      \"Cannot resolve @fairfox/polly from here. Run `polly mutate init` in a project that depends on @fairfox/polly.\"\n    );\n  }\n\n  const mutate = detectMutate(projectDir);\n  const testGlob = detectTestGlob(projectDir);\n  if (!existsSync(join(projectDir, \"src\"))) {\n    warnings.push(\"no src/ directory — adjust the `mutate` globs to point at your source\");\n  }\n  if (!existsSync(join(projectDir, \"tests\")) && !existsSync(join(projectDir, \"test\"))) {\n    warnings.push(`no tests/ directory — using \"${testGlob}\"; adjust bun.testFiles if needed`);\n  }\n\n  if (existsSync(configPath) && !opts.force) {\n    return { configPath, created: false, pluginRef, mutate, testGlob, warnings };\n  }\n\n  // Note: redundancy/subsumption need the no-bail patched bun runner (disableBail\n  // + coverageAnalysis \"all\"); without the patch the matrix is partial and\n  // `polly mutate report` degrades to score + gaps + theatre.\n  const config = {\n    testRunner: \"bun\",\n    bun: { testFiles: [testGlob], timeout: 30000 },\n    plugins: [\"stryker-mutator-bun-runner\", pluginRef],\n    ignorers: [\"polly-verify\"],\n    coverageAnalysis: \"all\",\n    disableBail: true,\n    reporters: [\"json\", \"clear-text\"],\n    mutate,\n    thresholds: { high: 90, low: 70, break: null },\n    ignorePatterns: [\n      \"**/node_modules/**\",\n      \"**/dist/**\",\n      \"**/.git/**\",\n      \"**/.stryker-tmp/**\",\n      \"**/reports/**\",\n    ],\n    timeoutMS: 60000,\n    concurrency: 4,\n  };\n  await Bun.write(configPath, `${JSON.stringify(config, null, 2)}\\n`);\n  return { configPath, created: true, pluginRef, mutate, testGlob, warnings };\n}\n",
+    "/**\n * Orchestration for `polly mutate run` / `report`: spawn Stryker, then read the\n * mutation report and produce the useless-test analysis — gating the redundancy\n * /subsumption sections on a complete (no-bail) kill matrix.\n */\nimport { resolve } from \"node:path\";\nimport type { MutateConfig } from \"./config.ts\";\nimport { buildDb, loadMutationReport } from \"./ingest.ts\";\nimport { report } from \"./report.ts\";\nimport { isMatrixComplete } from \"./verify-matrix.ts\";\n\n/** Run Stryker against the resolved config. Inherits stdio for the live reporter; returns the exit code. */\nexport async function runStryker(cfg: MutateConfig): Promise<number> {\n  // Pass --configFile only when the located config is NOT the auto-discoverable\n  // root stryker.conf.json — that keeps a bare repo run identical to `stryker run`.\n  const autoDiscoverable = cfg.strykerConfigPath === resolve(cfg.cwd, \"stryker.conf.json\");\n  const configFlag =\n    cfg.strykerConfigPath && !autoDiscoverable ? [\"--configFile\", cfg.strykerConfigPath] : [];\n  const proc = Bun.spawn([\"bunx\", \"stryker\", \"run\", ...configFlag], {\n    cwd: cfg.cwd,\n    stdout: \"inherit\",\n    stderr: \"inherit\",\n    stdin: \"inherit\",\n    env: process.env,\n  });\n  return await proc.exited;\n}\n\n/** Build the useless-test report from an existing mutation.json (no Stryker run). */\nexport async function reportFromFile(cfg: MutateConfig): Promise<string> {\n  if (!(await Bun.file(cfg.reportPath).exists())) {\n    throw new Error(\n      `no mutation report at ${cfg.reportPath}. Run 'polly mutate run' (or 'bun run mutation') first, or pass --report <path>.`\n    );\n  }\n  const mreport = await loadMutationReport(cfg.reportPath);\n  const db = buildDb(mreport, cfg.dbPath);\n  try {\n    return report(db, { matrixComplete: isMatrixComplete(mreport) });\n  } finally {\n    db.close();\n  }\n}\n\n/**\n * If the Stryker config doesn't already load polly's verify-primitive ignorer,\n * return a one-line tip. The ignorer must be in the config before the run (it's\n * read at Stryker startup), so this advises rather than mutating the user's config.\n */\nexport async function presetAdvisory(cfg: MutateConfig): Promise<string | null> {\n  if (!cfg.strykerConfigPath?.endsWith(\".json\")) return null;\n  try {\n    const conf = (await Bun.file(cfg.strykerConfigPath).json()) as unknown as {\n      plugins?: string[];\n    };\n    if ((conf.plugins ?? []).includes(\"@fairfox/polly/stryker\")) return null;\n    return (\n      \"Tip: spread pollyStrykerPreset (from @fairfox/polly/stryker) into your Stryker config — \" +\n      \"verify primitives (requires/ensures/…) are runtime no-ops and their mutants always survive, \" +\n      \"dragging the score down with noise. See polly#143.\"\n    );\n  } catch {\n    return null;\n  }\n}\n",
+    "/**\n * Test-debt report: derive the three signals from the kill matrix.\n *\n *   gaps        survived mutants — code no test pins (the Stryker direction)\n *   redundancy  tests/files whose every kill is also caught elsewhere\n *   theatre     covered-but-survived — code a test runs but no test detects\n *               (the Survived status under coverageAnalysis \"all\")\n *\n * Redundancy is reported at BOTH file and case level. Decisions are keyed at\n * file level (stable identity); case level is the drill-down.\n */\nimport type { Database } from \"bun:sqlite\";\nimport { buildDb, loadMutationReport, queryAll, queryGet } from \"./ingest.ts\";\n\ntype SubsumedCase = { file: string; name: string; total: number };\ntype LineCount = { line: number; mutator: string; n: number };\n\n/** Greedy set cover: smallest set of `units` whose kill-sets cover all killed mutants. */\n// biome-ignore lint/complexity/noExcessiveCognitiveComplexity: a textbook greedy set-cover loop — clearer whole than split.\nfunction greedyCover(units: Map<string, Set<string>>, universe: Set<string>): string[] {\n  const remaining = new Set(universe);\n  const chosen: string[] = [];\n  const pool = new Map([...units].map(([k, v]) => [k, new Set(v)]));\n  while (remaining.size > 0) {\n    let best: string | null = null;\n    let bestGain = 0;\n    for (const [unit, set] of pool) {\n      let gain = 0;\n      for (const m of set) if (remaining.has(m)) gain++;\n      if (gain > bestGain) {\n        bestGain = gain;\n        best = unit;\n      }\n    }\n    if (best === null || bestGain === 0) break; // remaining mutants killed by nobody (shouldn't happen for killed set)\n    chosen.push(best);\n    for (const m of pool.get(best) ?? []) remaining.delete(m);\n    pool.delete(best);\n  }\n  return chosen;\n}\n\n// biome-ignore lint/complexity/noExcessiveCognitiveComplexity: one report builder emitting all sections in order — splitting would scatter the shared db/out.\nexport function report(db: Database, opts: { matrixComplete?: boolean } = {}): string {\n  // Defaults to true so `report(db)` is byte-identical to before (the parity\n  // guard depends on this). When false — the kill matrix is partial (an\n  // unpatched/bail runner) — the redundancy/subsumption sections would lie, so\n  // they are suppressed and a warning shown; score/gaps/theatre still hold.\n  const matrixComplete = opts.matrixComplete ?? true;\n  const out: string[] = [];\n  const p = (s = \"\") => out.push(s);\n\n  // --- summary ---\n  const tot = queryGet<{\n    n: number;\n    killed: number;\n    survived: number;\n    timeout: number;\n    nocov: number;\n  }>(\n    db,\n    \"SELECT count(*) n, sum(status='Killed') killed, sum(status='Survived') survived, sum(status='Timeout') timeout, sum(status='NoCoverage') nocov FROM mutants\"\n  ) ?? { n: 0, killed: 0, survived: 0, timeout: 0, nocov: 0 };\n  const nTests = queryGet<{ n: number }>(db, \"SELECT count(*) n FROM tests\")?.n ?? 0;\n  const detected = tot.killed + tot.timeout;\n  const score = ((detected / (tot.n - tot.nocov || 1)) * 100).toFixed(1);\n  p(\n    `MUTATION  score ${score}%   ${tot.killed} killed · ${tot.timeout} timeout · ${tot.survived} survived · ${tot.nocov} no-coverage   (${tot.n} mutants, ${nTests} tests)`\n  );\n\n  if (matrixComplete) {\n    // --- kill-multiplicity: how much slack is in the matrix ---\n    const mult = queryAll<{ bucket: string; n: number }>(\n      db,\n      `\n\t\t\tSELECT CASE WHEN c=1 THEN '1' WHEN c=2 THEN '2' WHEN c BETWEEN 3 AND 5 THEN '3-5' ELSE '6+' END bucket, count(*) n\n\t\t\tFROM (SELECT mutant_id, count(*) c FROM kills GROUP BY mutant_id)\n\t\t\tGROUP BY bucket ORDER BY min(c)`\n    );\n    p(`\\nKILL MULTIPLICITY  (killers per killed mutant — higher = more redundancy slack)`);\n    for (const r of mult) p(`  killed by ${String(r.bucket).padStart(3)} test(s): ${r.n}`);\n\n    // --- redundancy ratio via greedy cover (case + file) ---\n    const universe = new Set(\n      queryAll<{ mutant_id: string }>(db, \"SELECT DISTINCT mutant_id FROM kills\").map(\n        (r) => r.mutant_id\n      )\n    );\n    const byTest = new Map<string, Set<string>>();\n    for (const r of queryAll<{ test_id: string; mutant_id: string }>(\n      db,\n      \"SELECT test_id, mutant_id FROM kills\"\n    )) {\n      const set = byTest.get(r.test_id) ?? new Set<string>();\n      byTest.set(r.test_id, set);\n      set.add(r.mutant_id);\n    }\n    const byFile = new Map<string, Set<string>>();\n    for (const r of queryAll<{ file: string; mid: string }>(\n      db,\n      \"SELECT t.file file, k.mutant_id mid FROM kills k JOIN tests t ON t.id=k.test_id\"\n    )) {\n      const set = byFile.get(r.file) ?? new Set<string>();\n      byFile.set(r.file, set);\n      set.add(r.mid);\n    }\n    const caseCover = greedyCover(byTest, universe);\n    const fileCover = greedyCover(byFile, universe);\n    p(`\\nREDUNDANCY RATIO  (tests that kill something ÷ minimal covering set)`);\n    p(\n      `  case level: ${byTest.size} killing tests → ${caseCover.length} needed   (${(byTest.size / Math.max(1, caseCover.length)).toFixed(2)}×, ~${byTest.size - caseCover.length} prunable)`\n    );\n    p(\n      `  file level: ${byFile.size} killing files → ${fileCover.length} needed   (${(byFile.size / Math.max(1, fileCover.length)).toFixed(2)}×, ~${byFile.size - fileCover.length} prunable)`\n    );\n\n    // --- fully subsumed FILES (every mutant they kill is killed elsewhere too) ---\n    const subsumedFiles = queryAll<{ file: string; kills: number }>(\n      db,\n      `\n\t\t\tWITH file_kill AS (SELECT DISTINCT t.file file, k.mutant_id mid FROM kills k JOIN tests t ON t.id=k.test_id),\n\t\t\t     owner AS (SELECT mid, count(DISTINCT file) nf, min(file) only_file FROM file_kill GROUP BY mid)\n\t\t\tSELECT fk.file, count(DISTINCT fk.mid) kills,\n\t\t\t       sum(CASE WHEN o.nf=1 THEN 1 ELSE 0 END) unique_kills\n\t\t\tFROM file_kill fk JOIN owner o ON o.mid=fk.mid\n\t\t\tGROUP BY fk.file HAVING unique_kills=0 ORDER BY kills DESC`\n    );\n    p(`\\nSUBSUMED FILES  (file-level identity — safe-to-review deletion candidates)`);\n    if (subsumedFiles.length === 0)\n      p(`  none — every test file kills at least one mutant no other file catches`);\n    for (const r of subsumedFiles) p(`  ${r.file}  (${r.kills} kills, 0 unique)`);\n\n    // --- fully subsumed CASES (drill-down) ---\n    const subsumedCases = queryAll<SubsumedCase>(\n      db,\n      `\n\t\t\tWITH mk AS (SELECT mutant_id, count(*) c FROM kills GROUP BY mutant_id),\n\t\t\t     tk AS (SELECT test_id, count(*) total, sum(CASE WHEN mk.c=1 THEN 1 ELSE 0 END) uniq\n\t\t\t            FROM kills JOIN mk USING(mutant_id) GROUP BY test_id)\n\t\t\tSELECT t.file, t.name, tk.total FROM tk JOIN tests t ON t.id=tk.test_id\n\t\t\tWHERE tk.total>0 AND tk.uniq=0 ORDER BY t.file, tk.total DESC`\n    );\n    const byFileCases = new Map<string, SubsumedCase[]>();\n    for (const r of subsumedCases) {\n      const rows = byFileCases.get(r.file) ?? [];\n      byFileCases.set(r.file, rows);\n      rows.push(r);\n    }\n    p(\n      `\\nSUBSUMED CASES  (${subsumedCases.length} individual tests whose every kill is caught elsewhere)`\n    );\n    for (const [file, rows] of byFileCases) {\n      p(`  ${file}`);\n      for (const r of rows) p(`      “${r.name}” (${r.total} kills, 0 unique)`);\n    }\n  } else {\n    p(`\\n⚠ KILL MATRIX INCOMPLETE — redundancy/subsumption analysis suppressed.`);\n    p(`  Every mutant has at most one recorded killer, so \"which tests are redundant\"`);\n    p(`  cannot be derived. This needs the no-bail patched Bun runner (not shipped with`);\n    p(\n      `  @fairfox/polly). Run 'polly mutate verify' to diagnose. Score/gaps/theatre below still hold.`\n    );\n  }\n\n  // Under coverageAnalysis \"all\", Stryker classifies a non-killed mutant as\n  // NoCoverage (no test runs it — a true gap) or Survived (a test runs it but\n  // nothing detects the mutation — theatre). That status split IS the\n  // gap/theatre distinction; it requires coverage to be on (see README).\n  const srcFile = queryGet<{ file: string }>(db, \"SELECT file FROM mutants LIMIT 1\")?.file;\n\n  // --- gaps: code no test even executes ---\n  const gaps = queryAll<LineCount>(\n    db,\n    \"SELECT line, mutator, count(*) n FROM mutants WHERE status='NoCoverage' GROUP BY line, mutator ORDER BY line\"\n  );\n  const gapTotal = gaps.reduce((a, r) => a + r.n, 0);\n  p(`\\nGAPS  (NoCoverage — no test executes this code: ${gapTotal})`);\n  if (gapTotal === 0) p(`  none — every mutable location is reached by some test`);\n  for (const r of gaps) p(`  ${srcFile}:${r.line}  ${r.mutator}${r.n > 1 ? ` ×${r.n}` : \"\"}`);\n\n  // --- theatre: covered but survived ---\n  const theatre = queryAll<LineCount>(\n    db,\n    \"SELECT line, mutator, count(*) n FROM mutants WHERE status='Survived' GROUP BY line, mutator ORDER BY line\"\n  );\n  const theatreTotal = theatre.reduce((a, r) => a + r.n, 0);\n  p(`\\nTHEATRE  (Survived — code is covered but no test detects the mutation: ${theatreTotal})`);\n  if (theatreTotal === 0) p(`  none`);\n  for (const r of theatre) p(`  ${srcFile}:${r.line}  ${r.mutator}${r.n > 1 ? ` ×${r.n}` : \"\"}`);\n\n  return out.join(\"\\n\");\n}\n\nif (import.meta.main) {\n  const reportPath = process.argv[2] ?? \"reports/mutation/mutation.json\";\n  const db = buildDb(await loadMutationReport(reportPath), \"reports/test-debt.sqlite\");\n  console.log(report(db));\n  db.close();\n}\n",
+    "/**\n * Verification artefact for the kill-matrix contract.\n *\n * The whole useless-test analysis rests on one fact: the patched bun runner\n * emits a COMPLETE kill matrix — every test that detects a mutant appears in\n * killedBy, not just the first. That depends on a pinned pair: (Bun version,\n * plugin version + our patch). A Bun upgrade that changes JUnit output, or a\n * patch that stops applying, would silently collapse killedBy to one id each —\n * a green board with the redundancy signal quietly dead (the classic trap).\n *\n * `verifyMatrix` runs the full contract and returns the result; `isMatrixComplete`\n * is the side-effect-free gate the report path consults to decide whether the\n * redundancy/subsumption sections are trustworthy. Run the CLI form after any\n * bump of Bun or the plugin:\n *\n *   polly mutate verify          # uses the existing report\n *   polly mutate verify --run    # runs stryker first\n */\nimport { loadMutationReport, type MutationReport } from \"./ingest.ts\";\n\nconst DEFAULT_REPORT = \"reports/mutation/mutation.json\";\n\nexport interface MatrixCheck {\n  ok: boolean;\n  checks: { name: string; ok: boolean; detail: string }[];\n}\n\n/**\n * Side-effect-free gate: is the kill matrix trustworthy for redundancy /\n * subsumption analysis? True only when\n *   (a) some killed mutant has >1 killer — proof the no-bail patched runner\n *       recorded EVERY killer, not just the first (verifyMatrix check #4), and\n *   (b) coverage was collected — not every mutant is NoCoverage, which would\n *       mean the coverage dump broke (verifyMatrix check #5).\n * Without both, REDUNDANCY/SUBSUMED would be computed off a partial matrix and\n * lie, so the report path falls back to score + gaps + theatre only.\n */\nexport function isMatrixComplete(report: MutationReport): boolean {\n  const mutants = Object.values(report.files).flatMap((f) => f.mutants);\n  if (mutants.length === 0) return false;\n  const killed = mutants.filter((m) => m.status === \"Killed\");\n  const multiKiller = killed.some((m) => (m.killedBy ?? []).length > 1);\n  const noCov = mutants.filter((m) => m.status === \"NoCoverage\").length;\n  const coverageCollected = noCov < mutants.length;\n  return multiKiller && coverageCollected;\n}\n\n/**\n * Run the full kill-matrix contract (all five checks), optionally running a\n * fresh Stryker pass first. Returns the result rather than exiting, so callers\n * decide what to do with it; the `import.meta.main` wrapper prints and sets the\n * exit code.\n */\nexport async function verifyMatrix(\n  opts: { reportPath?: string; run?: boolean; strykerConfig?: string } = {}\n): Promise<MatrixCheck> {\n  const reportPath = opts.reportPath ?? DEFAULT_REPORT;\n\n  if (opts.run) {\n    console.log(\"Running mutation pass (this can take many minutes for a large mutate set)...\");\n    const cmd = [\n      \"bunx\",\n      \"stryker\",\n      \"run\",\n      ...(opts.strykerConfig ? [\"--configFile\", opts.strykerConfig] : []),\n    ];\n    const proc = Bun.spawn(cmd, { stdout: \"inherit\", stderr: \"inherit\" });\n    const code = await proc.exited;\n    if (code !== 0) {\n      return { ok: false, checks: [{ name: \"stryker run\", ok: false, detail: `exited ${code}` }] };\n    }\n  }\n\n  if (!(await Bun.file(reportPath).exists())) {\n    return {\n      ok: false,\n      checks: [\n        {\n          name: \"report exists\",\n          ok: false,\n          detail: `no report at ${reportPath}. Run with --run, or 'bun run mutation' first.`,\n        },\n      ],\n    };\n  }\n\n  const report = await loadMutationReport(reportPath);\n  const checks: { name: string; ok: boolean; detail: string }[] = [];\n  const add = (name: string, ok: boolean, detail: string) => checks.push({ name, ok, detail });\n\n  // 1. schema present\n  add(\"schema version present\", !!report.schemaVersion, `schemaVersion=${report.schemaVersion}`);\n\n  // 2. testFiles keyed by real paths, not the \"\" bucket (file-level identity intact)\n  const tfKeys = Object.keys(report.testFiles ?? {});\n  const realPaths = tfKeys.filter((k) => k && k !== \"(unknown)\");\n  add(\n    \"testFiles keyed by real paths\",\n    realPaths.length > 0 && !tfKeys.includes(\"\"),\n    `${realPaths.length} file(s): ${realPaths.slice(0, 2).join(\", \")}${realPaths.length > 2 ? \"…\" : \"\"}`\n  );\n\n  // 3. test ids resolve\n  const testIds = new Set(\n    Object.values(report.testFiles ?? {}).flatMap((tf) => tf.tests.map((t) => t.id))\n  );\n  const mutants = Object.values(report.files).flatMap((f) => f.mutants);\n  const killed = mutants.filter((m) => m.status === \"Killed\");\n  const danglingKb = killed.filter((m) => (m.killedBy ?? []).some((id) => !testIds.has(id)));\n  add(\n    \"every killedBy id resolves to a test\",\n    danglingKb.length === 0,\n    `${danglingKb.length} dangling`\n  );\n\n  // 4. THE contract: a complete matrix means some killed mutant has >1 killer.\n  //    If bail silently re-engaged, every killedBy would have length 1.\n  const withKb = killed.filter((m) => (m.killedBy ?? []).length > 0);\n  const multi = killed.filter((m) => (m.killedBy ?? []).length > 1);\n  add(\n    \"killed mutants carry killedBy\",\n    killed.length > 0 && withKb.length === killed.length,\n    `${withKb.length}/${killed.length}`\n  );\n  add(\n    \"matrix is complete (no-bail): >1 killer exists\",\n    multi.length > 0,\n    `${multi.length} mutant(s) killed by >1 test — collapses to 0 if bail re-engages`\n  );\n\n  // 5. coverage extraction works: if the afterAll dump fails, the coverage map is\n  //    empty and Stryker marks EVERY mutant NoCoverage (theatre/gap split dies).\n  const noCov = mutants.filter((m) => m.status === \"NoCoverage\").length;\n  add(\n    \"coverage collected (not all NoCoverage)\",\n    noCov < mutants.length,\n    `${noCov}/${mutants.length} NoCoverage — all-NoCoverage means the coverage dump broke`\n  );\n\n  return { ok: checks.every((c) => c.ok), checks };\n}\n\nif (import.meta.main) {\n  const result = await verifyMatrix({ run: process.argv.includes(\"--run\") });\n  console.log(\"\\nKill-matrix contract:\");\n  for (const c of result.checks) {\n    console.log(`  ${c.ok ? \"✓\" : \"✗\"} ${c.name}  (${c.detail})`);\n  }\n  if (!result.ok) {\n    console.log(\n      \"\\n✗ Contract broken. The pinned pair has drifted — re-check Bun version and that the patch applies (bun install).\"\n    );\n    process.exit(1);\n  }\n  console.log(\"\\n✓ Kill-matrix contract holds.\");\n}\n",
+    "#!/usr/bin/env bun\n/**\n * `polly mutate` — run Stryker mutation testing and surface useless/redundant\n * tests (the inverse reading of the kill matrix). Thin dispatcher over the\n * reusable functions in this directory.\n */\nimport { parseMutateArgs } from \"./args.ts\";\nimport { resolveMutateConfig } from \"./config.ts\";\nimport { decide, status } from \"./decisions.ts\";\nimport { buildDb, loadMutationReport } from \"./ingest.ts\";\nimport { initConfig } from \"./init.ts\";\nimport { presetAdvisory, reportFromFile, runStryker } from \"./run.ts\";\nimport { verifyMatrix } from \"./verify-matrix.ts\";\n\nconst HELP = `polly mutate — mutation testing + useless-test detection\n\nUsage:\n  polly mutate init [--force]        Scaffold a stryker.conf.json for this project\n  polly mutate [run]                 Run Stryker, then print the useless-test report\n  polly mutate report                Print the report from an existing mutation.json\n  polly mutate decisions             Review verdicts: needs-review / stale / settled\n  polly mutate decisions decide <file> <keep|prune|rewrite|investigate> \"<rationale>\"\n  polly mutate verify [--run]        Assert the kill-matrix contract (exit 1 on drift)\n  polly mutate help                  Show this help\n\nFlags:\n  --config <path>     Stryker config (default: auto-discovered)\n  --report <path>     mutation report JSON (default: reports/mutation/mutation.json)\n  --decisions <path>  verdict log (default: .polly/test-debt/decisions.jsonl)\n  --db <path>         intermediate SQLite (default: in-memory)\n  --no-report         'run' only — skip the analysis\n  -h, --help\n\nThe redundancy/subsumption sections need a COMPLETE kill matrix (the no-bail\npatched Bun runner). Without it the report degrades to score + gaps + theatre;\n'polly mutate verify' diagnoses the matrix.`;\n\nasync function openDb(\n  reportPath: string,\n  dbPath: string\n): Promise<ReturnType<typeof buildDb> | null> {\n  if (!(await Bun.file(reportPath).exists())) {\n    console.log(\n      `no mutation report at ${reportPath}. Run 'polly mutate run' first, or pass --report <path>.`\n    );\n    return null;\n  }\n  return buildDb(await loadMutationReport(reportPath), dbPath);\n}\n\n// biome-ignore lint/complexity/noExcessiveCognitiveComplexity: a flat verb dispatcher — the branches are the command surface.\nasync function main(): Promise<number> {\n  const args = parseMutateArgs(process.argv.slice(2));\n  if (args.help) {\n    console.log(HELP);\n    return 0;\n  }\n\n  const cwd = process.cwd();\n  const cfg = await resolveMutateConfig(cwd, args);\n\n  switch (args.verb) {\n    case \"init\": {\n      const result = await initConfig(cwd, { force: args.force });\n      if (!result.created) {\n        console.log(\n          `stryker.conf.json already exists at ${result.configPath}. Re-run with --force to overwrite.`\n        );\n        return 1;\n      }\n      console.log(`✓ wrote ${result.configPath}`);\n      console.log(`  plugin:    ${result.pluginRef}`);\n      console.log(`  mutate:    ${result.mutate.join(\", \")}`);\n      console.log(`  testFiles: ${result.testGlob}`);\n      for (const w of result.warnings) console.log(`  ⚠ ${w}`);\n      console.log(\"\\nNext: polly mutate run\");\n      return 0;\n    }\n\n    case \"run\": {\n      const tip = await presetAdvisory(cfg);\n      if (tip) console.log(`${tip}\\n`);\n      const code = await runStryker(cfg);\n      if (code !== 0) return code;\n      if (args.noReport) return 0;\n      console.log(`\\n${await reportFromFile(cfg)}`);\n      return 0;\n    }\n\n    case \"report\": {\n      console.log(await reportFromFile(cfg));\n      return 0;\n    }\n\n    case \"decisions\": {\n      const db = await openDb(cfg.reportPath, cfg.dbPath);\n      if (!db) return 1;\n      try {\n        if (args.rest[0] === \"decide\") {\n          const [, file, verdict, ...r] = args.rest;\n          if (!file || !verdict) {\n            console.log(\n              'usage: polly mutate decisions decide <file> <keep|prune|rewrite|investigate> \"<rationale>\"'\n            );\n            return 1;\n          }\n          await decide(file, verdict, r.join(\" \").replace(/^\"|\"$/g, \"\"), db, cfg.decisionsPath);\n        } else {\n          console.log(await status(db, cfg.decisionsPath));\n        }\n      } finally {\n        db.close();\n      }\n      return 0;\n    }\n\n    case \"verify\": {\n      const result = await verifyMatrix({\n        reportPath: cfg.reportPath,\n        run: args.run,\n        strykerConfig: cfg.strykerConfigPath ?? undefined,\n      });\n      console.log(\"\\nKill-matrix contract:\");\n      for (const c of result.checks) console.log(`  ${c.ok ? \"✓\" : \"✗\"} ${c.name}  (${c.detail})`);\n      if (!result.ok) {\n        console.log(\n          \"\\n✗ Contract broken. The pinned pair has drifted — re-check Bun version and that the patch applies (bun install).\"\n        );\n        return 1;\n      }\n      console.log(\"\\n✓ Kill-matrix contract holds.\");\n      return 0;\n    }\n\n    default:\n      console.log(`Unknown subcommand: ${args.verb}\\n`);\n      console.log(HELP);\n      return 1;\n  }\n}\n\nmain()\n  .then((code) => process.exit(code))\n  .catch((err) => {\n    console.log(`\\n❌ ${err instanceof Error ? err.message : String(err)}`);\n    process.exit(1);\n  });\n"
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+  "debugId": "768AC36DADFC60B164756E2164756E21",
+  "names": []
+}

package/dist/tools/mutate/src/config.d.ts

@@ -0,0 +1,13 @@
+import type { MutateArgs } from "./args.ts";
+export interface MutateConfig {
+    cwd: string;
+    /** The Stryker config to use — explicit `--config`, else the first discovered. Null if none found. */
+    strykerConfigPath: string | null;
+    /** mutation-testing-report-schema JSON the analysis reads. */
+    reportPath: string;
+    /** Intermediate SQLite db (":memory:" by default; a path persists it). */
+    dbPath: string;
+    /** Version-controlled human-verdict log. */
+    decisionsPath: string;
+}
+export declare function resolveMutateConfig(cwd: string, args: MutateArgs): Promise<MutateConfig>;

package/dist/tools/mutate/src/decisions.d.ts

@@ -0,0 +1,34 @@
+/**
+ * Decisions log — the version-controlled human-judgement layer.
+ *
+ * The signals (kill matrix, subsumption) are derived and regenerable; they live
+ * in the gitignored SQLite db. *Decisions* about them — "this subsumed file is a
+ * legitimate set of input-class guards, keep it" — are precious, can't be
+ * regenerated, and are committed here as JSONL (one record per line: mergeable,
+ * diffable, append-only, last-write-wins per file).
+ *
+ * Identity is the test FILE (stable across describe restructuring; git tracks
+ * renames). Each decision stores two freshness stamps:
+ *   - hash:   a normalised content hash of the test file at decision time.
+ *             Differs → the test changed since you judged it → re-review.
+ *   - signal: the subsumption snapshot at decision time. Drifts (e.g. a test
+ *             elsewhere was deleted, so this file's kills became unique) → the
+ *             matrix around it changed → re-review.
+ *
+ * A decision is trusted only while BOTH still hold. That's what stops a "keep"
+ * verdict from silently outliving the reason it was made.
+ *
+ *   polly mutate decisions                          # status (the join)
+ *   polly mutate decisions decide <file> <verdict> "<rationale>"
+ *
+ * verdicts: keep | prune | rewrite | investigate
+ */
+import type { Database } from "bun:sqlite";
+export interface FileSignal {
+    kills: number;
+    uniqueKills: number;
+    subsumed: boolean;
+}
+export declare function fileSignals(db: Database): Map<string, FileSignal>;
+export declare function status(db: Database, logPath?: string): Promise<string>;
+export declare function decide(file: string, verdict: string, rationale: string, db: Database, logPath?: string): Promise<void>;

package/dist/tools/mutate/src/index.d.ts

@@ -0,0 +1,13 @@
+/**
+ * @fairfox/polly/mutate — programmatic surface for mutation-testing analysis.
+ *
+ * The CLI (`polly mutate`) is the primary entry point; this barrel exposes the
+ * reusable pieces for consumers who want to drive the analysis themselves:
+ * ingest a mutation report into the kill matrix, derive the useless-test signals,
+ * and assert the matrix contract.
+ */
+export { decide, type FileSignal, fileSignals, status } from "./decisions.ts";
+export { buildDb, type MutationReport } from "./ingest.ts";
+export { type InitResult, initConfig } from "./init.ts";
+export { report } from "./report.ts";
+export { isMatrixComplete, type MatrixCheck, verifyMatrix } from "./verify-matrix.ts";