@dzhechkov/harness-cli 0.8.25 → 0.8.26

package/src/cli.ts

@@ -5,8 +5,15 @@
  */
 
 import { parseNpmPackInventory, type InventorySource, type LocalInventoryResult } from '@dzhechkov/harness-core';
+// Fix-round 1 (Codex HIGH-1c, feature recall-short-terms): the ONE place `dz recall` prints an
+// empty result must name WHY — via the shared helper, not by re-deriving the decision. Routed
+// through harness-core's re-export (lead correction) rather than a new direct dependency on
+// `@dzhechkov/memory`: a new package-graph edge is a publishing-surface change outside this
+// feature's scope, and harness-core already depends on memory.
+import { noSearchableTermsReason } from '@dzhechkov/harness-core';
 import { appendFileSync, chmodSync, closeSync, constants as fsConstants, cpSync, existsSync, fstatSync, fsyncSync, lstatSync, mkdirSync, mkdtempSync, openSync, readFileSync, readSync, readdirSync, readlinkSync, realpathSync, renameSync, rmdirSync, rmSync, statSync, symlinkSync, unlinkSync, writeFileSync, writeSync, type Dirent } from 'node:fs';
-import { basename, dirname, extname, isAbsolute, join, relative, resolve, sep } from 'node:path';
+import { basename, dirname, extname, isAbsolute, join, relative, resolve, sep, posix as nodePosixPath } from 'node:path';
+const posixNormalize = nodePosixPath.normalize;
 import { fileURLToPath } from 'node:url';
 import { request as httpsRequest } from 'node:https';
 import { KNOWN_CLI_FLAGS } from './known-flags.js';
@@ -15,7 +22,7 @@ import { resolveInstallSpec } from './install-spec.js';
 import { dispatchedCommands, documentedCommands } from './command-inventory.js';
 import { execFile, execFileSync, execSync, spawn, spawnSync, type ChildProcess } from 'node:child_process';
 import { createHash, randomBytes } from 'node:crypto';
-import { homedir, hostname, tmpdir } from 'node:os';
+import { cpus, homedir, hostname, tmpdir } from 'node:os';
 import { createRequire } from 'node:module';
 import { isDeepStrictEqual } from 'node:util';
 import { JOURNAL_KINDS, formatLine, parseLine, selectWindow, appendWitnessed, type JournalKind, type JournalIo } from '@dzhechkov/harness-core';
@@ -65,6 +72,7 @@ import {
   runDoctor,
   runInit,
   discoverSkillIds,
+  loadSkillFromDir,
   resolveSelection,
   formatSelectRefusal,
   runIntegrationsVerify,
@@ -139,6 +147,7 @@ import {
   TARGET_SHORT_LABELS,
   applyLegStatus,
   applyLegReasonMessage,
+  probeApplyLeg,
   resolveAgentdbPath,
   WORKFLOW_TEMPLATES_RETIRED_MESSAGE,
   parsePlan,
@@ -558,6 +567,7 @@ import {
   REGISTRY_SELFCHECK_TESTS,
   buildMutationTestCommand,
   parseMutationRegistry,
+  registryEntriesAddedSince,
   applyMutationToText,
   attributeBaselineRedness,
   countFailingTests,
@@ -630,7 +640,7 @@ import {
 import type { OperatorProfile, Domain as ProfileDomain, Register as ProfileRegister } from '@dzhechkov/harness-core';
 import type { RecordKind, RecordDecision } from '@dzhechkov/harness-core';
 import type { CadenceWindow } from '@dzhechkov/harness-core';
-import type { MutationEntryResult, MutationObservation, MutationRegistryEntry } from '@dzhechkov/harness-core';
+import type { MutationEntryResult, MutationObservation, MutationRegistryEntry, MutationRegistry } from '@dzhechkov/harness-core';
 import type { SkillApplyFailure, SkillLoadFailure } from '@dzhechkov/harness-core';
 import type { ReqeDebt } from '@dzhechkov/harness-core';
 import type { ClassifyResultRow, ExecutionEvidence } from '@dzhechkov/harness-core';
@@ -752,7 +762,7 @@ Usage:
   dz profile [init|show|set|sync] [--json]   (WHO the assistant is talking to — per-user store at ~/.dz/profile.json (0600, NEVER in a project), delivered as a marked block in ~/.claude/CLAUDE.md so it loads in EVERY project, dz installed or not. init = five questions (language, register, deep/weak domains as comma lists — "networking (CCIE; NSX)" keeps the parenthetical as the note, Enter skips — teaches y/n with one re-ask, never a silent default); show ALWAYS prints the store path + age + drift verdict + the rendered block; set register|language|teaches <v> or set deep|weak add|rm <tag> [note] — register accepts the owner's own words (профи / профи лайт / просто), an unknown value is REFUSED naming the accepted set; sync re-writes the block (runs automatically after init/set; foreign content byte-for-byte, timestamped backup before every modifying write). The register changes FORM, never FACTS, and governs dialogue only — never ADRs/commits/QE reports; both rules are baked into the rendered block at every level. exit 0 done / 1 no profile or failed / 2 refused input)
   dz reqe [--slug <feature> [--done --report <f>]] [--json]   (the re-QE debt ledger: a usage-switched run whose Step-8 QE ran on the coder's OWN family records a debt; list debts, print the cross-family review brief, settle FAIL-CLOSED against a graded report — the settlement lands in 08_qe_report.md)
   dz qe-bridge --family claude --slug <feature> [--coder-family codex|claude] [--model <id>] [--files a,b] [--out <f>] [--timeout <s>] [--allow-same-family] [--json]   (the REVERSE QE bridge: run an INDEPENDENT Claude reviewer over a feature's Step-8 artifacts from ANY host — a Codex session included, plain shell, no Claude agent plane needed — and land a PARSED signoff. The reviewer runs ISOLATED: an EMPTY temp cwd plus --safe-mode --strict-mcp-config --tools '' --no-session-persistence, so no CLAUDE.md/skills/plugins/hooks/MCP load, and the verdict is read from the --output-format json RESULT ENVELOPE — text a session customization printed onto the same stdout can never become a signoff. Probes the model before trusting it; sends SCOPED extracts with a loud 200k-char ceiling (never silent truncation); the grade must AGREE across three LAST-anchored channels (terminal marker line, fenced qe-bridge-signoff JSON, the report's own GRADE line) AND the marker must be the FINAL content — empty, gradeless, self-contradicting or miscounted output is one of 17 NAMED failures with an audit record under features/<slug>/.fa-state/qe-bridge/ (runId, resolved executable + binOverride, prompt sha256, channel offsets, requestedOut, reportWritten, retained raw stdout; 0600 files in a 0700 dir), never a clean review. A --coder-family that contradicts the recorded reqe debt is refused. Writes features/<slug>/08b_reqe_report.md, which dz reqe --done settles unchanged. DISCLOSURE: the extracts you scope are sent to the Claude runtime; the bridge cannot classify secrets. DZ_QE_BRIDGE_CLAUDE_BIN is a TEST SEAM, not a flag. exit 0 signoff parsed (ANY grade — it reports, it does not gate) / 1 named failure / 2 usage)
-  dz mutation-gate [--package <dir>] [--registry <file>] [--test-cmd "<cmd>"] [--only <id[,id]>] [--timeout <ms>] [--rebaseline per-entry|final] [--keep-scratch] [--json]   (prove each NAMED protection has a test that DISCRIMINATES: copy the package to a scratch dir, verify the baseline suite is green, apply each registry mutation, run the suite, REQUIRE red, restore. The red must be BEHAVIOURAL: a mutation that no longer parses is MUTATION_UNPARSEABLE; a red run whose OWN output reports a test FILE failing to load (node --test file-level not-ok with exitCode, vitest Failed Suites) is MUTATION_LOAD_FATAL — the signal comes from the same run as the failing count, never from a separate isolated import; red output whose shape matches no known runner is INCONCLUSIVE (a runner-coverage gap, loud, never PROVEN); a count far above the entry's bound is OVER_FAILING; a restored tree that does not reproduce green makes the entry INCONCLUSIVE (flaky). Mutation writes are realpath-contained to the scratch copy: a symlink escape or a node_modules/ target is refused (exit 2), the real tree is never written. A mutation that does not apply, a green suite, or an inconclusive run is a FAILURE — never a skip. exit 0 all proven / 1 gate failed / 2 setup error)
+  dz mutation-gate [--package <dir>] [--registry <file>] [--test-cmd "<cmd>"] [--only <id[,id]>] [--touched <path[,path]>] [--added-since <git-ref>] [--timeout <ms>] [--max-workers <n>] [--rebaseline per-entry|final] [--keep-scratch] [--json]   (prove each NAMED protection has a test that DISCRIMINATES: '--max-workers' resolves flag > the registry's own 'maxWorkers' field > 'min(4, max(1, floor(cpus/2)))' (an invalid flag value — 0, negative, fractional, non-numeric — is a usage error, exit 2, never a silent default; fix-round 1), injects '--maxWorkers=<n>' right after 'vitest run' inside its own compound-command segment (unless that segment already names the flag; fix-round 1 — scoped detection, not a whole-command substring check) and sets 'VITEST_MAX_WORKERS=<n>' in the env regardless — an uncapped full-suite baseline/mutant run at vitest's default worker count (= cpu cores) has measured load 62-358 and <2GB free on an 8-core/16GB box under embedding-daemon tests, killing full overnight gate runs (0bb74d66); printed as 'mutation-gate: workers: <n> (<flag|registry|default>)', or 'mutation-gate: workers: n/a — test command is not vitest' when the command is not recognised as vitest. '--touched' selects entries whose 'file' matches one of the given paths, accepted in ANY of package-relative, './'-prefixed, absolute-inside-the-package, repo-relative, or backslash-separated form — all normalized to package-relative POSIX before matching (fix-round 1, AM-1); a path that resolves OUTSIDE the package is counted, never silently dropped, as '<K> outside package' in the 'selected N of M' line; '--added-since <ref>' selects entries whose id is not present in the registry as it read at that ref ('git show <ref>:<registry path>'): a registry genuinely ABSENT at that ref means every current entry counts as added (said explicitly); an unresolvable ref, any OTHER git failure, or an invalid/malformed base registry at that ref is a usage error (exit 2), never folded into "absent" (AM-3) — a feature scopes the gate to its own touched files and any entries it just added instead of the whole registry (MEASURED: an unscoped run over 358 entries on this repo's core package ran 30-40 minutes and hit the timeout wall, INCONCLUSIVE every time). The two selectors UNION and the result INTERSECTS with '--only' when both are given; an empty selection prints 'selected 0 of M entries (…)' and exits 0 — never a silent skip; '--json' always carries a 'selection' object ({selected, total, touched, addedSince, base, outsidePackage}) on every scoped run (AM-4). copy the package to a scratch dir, verify the baseline suite is green, apply each registry mutation, run the suite, REQUIRE red, restore. The red must be BEHAVIOURAL: a mutation that no longer parses is MUTATION_UNPARSEABLE; a red run whose OWN output reports a test FILE failing to load (node --test file-level not-ok with exitCode, vitest Failed Suites) is MUTATION_LOAD_FATAL — the signal comes from the same run as the failing count, never from a separate isolated import; red output whose shape matches no known runner is INCONCLUSIVE (a runner-coverage gap, loud, never PROVEN); a count far above the entry's bound is OVER_FAILING; a restored tree that does not reproduce green makes the entry INCONCLUSIVE (flaky). Mutation writes are realpath-contained to the scratch copy: a symlink escape or a node_modules/ target is refused (exit 2), the real tree is never written. A mutation that does not apply, a green suite, or an inconclusive run is a FAILURE — never a skip. exit 0 all proven / 1 gate failed / 2 setup error)
   dz backlog add "<idea>" [--effort 1-5] [--proposal <text>] [--dry-run] [--allow-cold-start] [--project <dir>] [--json]   (capture an idea: semantic dedup against existing ideas via the Brain vector engine (DUPLICATE>=0.92 merges, RELATED links, NEW creates) + GoalMap alignment; --dry-run classifies without writing)
   dz backlog list [--status <s>] [--goal <id>] [--project <dir>] [--json]   (list captured ideas, filterable by status/goal)
   dz backlog show <id> [--project <dir>] [--json]                          (full record for one idea)
@@ -855,6 +865,13 @@ export type MutationGateRunner = (
     readonly timeoutMs: number;
     readonly phase: 'baseline' | 'mutation' | 'rebaseline' | 'final-rebaseline';
     readonly entryId?: string;
+    /**
+     * mutation-gate-baseline-honesty FR-3: the extra env vars the REAL executor would set on top of
+     * `process.env` for this run — currently just `VITEST_MAX_WORKERS`, set unconditionally
+     * regardless of whether the test command is recognised as vitest (a non-vitest command still
+     * gets the env var; only the command-string injection is vitest-gated).
+     */
+    readonly env: Readonly<Record<string, string>>;
   },
 ) => MutationGateRunnerObservation;
 
@@ -2599,6 +2616,41 @@ async function cmdInstall(
   if (root.layout === 'npx-template' && root.hasCompanionAssets) {
     write(`  note: ${pkg} also ships commands/hooks/agents — \`npx -y ${pkg} init\` installs the full kit.`);
   }
+  // Junk-skip summary (feature skills-walk-symlinks-and-junk, FR-2/AC-3). `report.skills[].skipped`
+  // above is a WRITE outcome (an existing file not overwritten without --force) — a different
+  // question from "did this skill directory contain build/cache junk that never became an asset at
+  // all". Re-walk each discovered skill (a cheap second READ — `loadSkillFromDir` already did this
+  // once inside `runInit`'s `adapter.compile`, this adds no write) to surface that count without
+  // reshaping `InitReport`. Silent at N=0 (AC-3): most packages ship no junk and must print nothing.
+  // fix-round 1 MEDIUM-4: this counts ENTRIES, not files. A skipped junk DIRECTORY (e.g.
+  // `__pycache__`) is exactly one entry here even though it may hold many files underneath —
+  // `walkFiles` never descends into a skipped junk directory to count those (see skills.ts),
+  // so a per-file count would be a number this code cannot honestly produce. The wording and
+  // the trailing `/` on directory paths say so, instead of implying "file" for something that
+  // may be a whole tree.
+  let junkSkippedCount = 0;
+  const junkSkippedPaths: string[] = [];
+  for (const id of discoverSkillIds(root.dir)) {
+    let skill;
+    try {
+      skill = loadSkillFromDir(root.dir, id);
+    } catch {
+      continue; // unparseable skills are reported separately via report.failures below
+    }
+    for (const entry of skill.skipped ?? []) {
+      if (!entry.reason.startsWith('junk')) continue; // broken-symlink/cycle/escape skips are a different concern (FR-1/AM-8)
+      junkSkippedCount += 1;
+      const shownPath = relative(pkgDir, entry.path).split('\\').join('/');
+      const isDir = entry.reason.startsWith('junk directory');
+      junkSkippedPaths.push(isDir ? `${shownPath}/` : shownPath);
+    }
+  }
+  if (junkSkippedCount > 0) {
+    const shown = junkSkippedPaths.slice(0, 5).join(', ');
+    const more = junkSkippedPaths.length > 5 ? `, … (+${junkSkippedPaths.length - 5} more)` : '';
+    const noun = junkSkippedCount === 1 ? 'entry' : 'entries';
+    write(`skills: skipped ${junkSkippedCount} junk ${noun} (${shown}${more})`);
+  }
   // Skip-and-collect at install time (D1 / the report's D2 amendment): the offending
   // SKILL.md came out of the DOWNLOADED TARBALL, so the path is rendered relative to
   // the package root (a `node_modules/**` absolute path is not actionable) and the
@@ -5061,7 +5113,18 @@ async function cmdRecall(
 
   if (hits.length === 0) {
     write(`dz recall "${shownQuery}"`);
-    write(`  No matching patterns (teach some with \`dz teach\`, or consolidate sessions).`);
+    // Fix-round 1 (Codex HIGH-1c): a query that tokenizes to literally nothing (pure
+    // punctuation/whitespace) is a DIFFERENT empty result than a query with real terms that
+    // simply matched no record — FR-3 requires the reason to be named, not folded into the same
+    // generic "no matching patterns" line. `noSearchableTermsReason` is the single source of
+    // truth for the decision (memory/src/tokenize.ts); this print site calls it rather than
+    // re-deriving "no searchable terms" from the query text itself.
+    const noTermsReason = noSearchableTermsReason(query);
+    if (noTermsReason !== undefined) {
+      write(`  no searchable terms in "${shownQuery}" (only punctuation/whitespace) — reason: ${noTermsReason}`);
+    } else {
+      write(`  No matching patterns (teach some with \`dz teach\`, or consolidate sessions).`);
+    }
     // The domain note must print here too (Codex QE #10): a --domain run with zero hits
     // silently said nothing about the domain, so the reader could not tell whether the
     // boost had been applied and found nothing, or had not run at all.
@@ -7989,7 +8052,7 @@ function cmdPublish(
 /*  ADR-001): computed from the declarative model, never hand-written  */
 /* ------------------------------------------------------------------ */
 
-function cmdParity(options: Map<string, string>, flags: Set<string>, write: Write, writeErr: WriteErr, cwd: string): number {
+async function cmdParity(options: Map<string, string>, flags: Set<string>, write: Write, writeErr: WriteErr, cwd: string): Promise<number> {
   const json = flags.has('json');
   if (flags.has('help')) {
     write('dz parity [--target <name>] [--json] — the computed feature×target map (never hand-written)');
@@ -8017,30 +8080,53 @@ function cmdParity(options: Map<string, string>, flags: Set<string>, write: Writ
     }
   }
 
-  // ADR-001 Decision 3 (feature setup-installs-apply-leg): `learning-apply` on `claude-code` is
-  // MEASURED, not declared — `hooks-prompt` is present for that ONE target only when
-  // `applyLegStatus(root).installed`. `computeParity` itself is untouched (FR-5); only the
-  // capability SET fed into it for this one cell differs from the static `TARGET_CAPABILITIES`.
-  // `applyLegStatus` never throws (fix round 1, Q3 finding: an unreadable helper used to be able to
-  // crash this command rather than degrade to a named remedy).
+  // ADR-001 Decision 3 (feature setup-installs-apply-leg), extended by `apply-leg-never-silent`
+  // Decision 3 (FR-4): `learning-apply` on `claude-code` is MEASURED, not declared — `hooks-prompt`
+  // is present for that ONE target only when the leg is OBSERVED to inject, not merely installed.
+  // Issue #2 was exactly this cell reading `full` while the leg injected nothing in every session
+  // but one: `applyLegStatus(root).installed` alone (file presence + structural wiring) is
+  // necessary but not sufficient — `probeApplyLeg` is the live end-to-end proof. `computeParity`
+  // itself is untouched (FR-5 of the earlier feature); only the capability SET fed into it for this
+  // one cell differs from the static `TARGET_CAPABILITIES`, exactly as before this feature.
+  // `applyLegStatus` never throws (fix round 1, Q3 finding); `probeApplyLeg` is only invoked when
+  // `installed` is true — a leg with missing/stale/unreadable helpers has nothing live to probe,
+  // and the pre-existing remedy for that state is unchanged.
   const applyLegStatusVal = applyLegStatus(cwd);
   const applyLegInstalled = applyLegStatusVal.installed;
+  // Codex round-2: `probeApplyLeg` may REJECT (temp dir, dynamic import, a throwing remover) — doctor
+  // catches that; parity must too, or a probe crash would crash `dz parity` instead of reading as
+  // "installed but silent: probe-error".
+  let applyLegProbe: Awaited<ReturnType<typeof probeApplyLeg>> | undefined;
+  if (applyLegInstalled) {
+    try {
+      applyLegProbe = await probeApplyLeg(cwd);
+    } catch (err) {
+      applyLegProbe = { ok: false, reason: `probe-error: ${err instanceof Error ? err.message : String(err)}`, elapsedMs: 0 };
+    }
+  }
+  const applyLegWorking = applyLegProbe?.ok === true;
   const matrix = buildParityMatrix().map((row) => {
-    if (row.feature.id !== 'learning-apply' || applyLegInstalled) return row;
+    if (row.feature.id !== 'learning-apply' || applyLegWorking) return row;
     const claudeCodeCaps = TARGET_CAPABILITIES['claude-code'].filter((c) => c !== 'hooks-prompt');
     return { feature: row.feature, cells: { ...row.cells, 'claude-code': computeParity(row.feature, claudeCodeCaps) } };
   });
-  // The "not installed" remedy — named ONLY for the one cell whose grant is a live measurement,
-  // never a blanket note for every `manual` cell (most targets are manual by DESIGN, not absence).
-  // `stale-version`/`unreadable` route through `applyLegReasonMessage` — the SAME text-producing
-  // function `dz doctor` uses for those two reasons (fix round 1, HIGH finding 2 / Q3 finding 7), so
-  // the two instruments cannot disagree about WHY a stale or broken install is not "full".
+  // The remedy — named ONLY for the one cell whose grant is a live measurement, never a blanket
+  // note for every `manual` cell (most targets are manual by DESIGN, not absence). Three distinct
+  // states, never conflated: NOT installed (stale-version/unreadable route through
+  // `applyLegReasonMessage`, the SAME text-producing function `dz doctor` uses for those two
+  // reasons, so the two instruments cannot disagree about WHY); installed but the live probe did
+  // NOT observe injection (FR-4's new "installed but silent" case, reason from `probeApplyLeg`
+  // itself — the SAME reason `dz doctor`'s live-probe row prints, so doctor and parity cannot
+  // disagree about a dead leg either); and the working case, where this function returns ''.
   const applyLegRemedy = (featureId: string, t: TargetName): string => {
-    if (featureId !== 'learning-apply' || t !== 'claude-code' || applyLegInstalled) return '';
-    if (applyLegStatusVal.reason === 'stale-version' || applyLegStatusVal.reason === 'unreadable') {
-      return ` — ${applyLegReasonMessage(applyLegStatusVal)}`;
+    if (featureId !== 'learning-apply' || t !== 'claude-code' || applyLegWorking) return '';
+    if (!applyLegInstalled) {
+      if (applyLegStatusVal.reason === 'stale-version' || applyLegStatusVal.reason === 'unreadable') {
+        return ` — ${applyLegReasonMessage(applyLegStatusVal)}`;
+      }
+      return ' — not installed — run dz setup --target claude-code --memory agentdb';
     }
-    return ' — not installed — run dz setup --target claude-code --memory agentdb';
+    return ` — installed but silent: ${applyLegProbe?.reason ?? 'unknown'}`;
   };
   // EVIDENCE staleness, folded into the report (fix round 2, R2-3). Derived from the records
   // themselves — no `codex --version`, no subprocess, so `dz parity` stays a deterministic function
@@ -12955,6 +13041,46 @@ function splitMutationGateOutputWrite(
   return 'path' in result ? { outputPath: result.path } : { outputError: result.error };
 }
 
+/** Fix-round 1 (AM-1, feature qe-step-gate-scoped-to-feature): a `--touched` path arrives in one of
+ * several shapes — package-relative POSIX (the common case, already correct as-is), with a leading
+ * `./`, as an ABSOLUTE path inside the package, or REPO-relative (e.g.
+ * `packages/@dzhechkov/harness-cli/src/x.ts`) — and on a POSIX host a caller may hand a backslash
+ * path too (a Windows-authored change list). MEASURED (Codex round-1 review): the pre-fix
+ * normalization only converted the native path separator, so any of the other shapes matched ZERO
+ * registry entries and the gate silently reported `selected 0` / exit 0 — the run looked clean while
+ * defending nothing. This resolves EVERY shape to the package-relative POSIX candidate(s) a registry
+ * entry's `file` is written in, and — when a path genuinely resolves outside `pkgDir` (an absolute
+ * path elsewhere, or a `../` that still escapes the package after a repo-relative reinterpretation)
+ * — reports it as `outside`, never a silent non-match indistinguishable from "the path doesn't
+ * exist".
+ */
+function normalizeTouchedPath(
+  raw: string,
+  pkgDir: string,
+  repoTop: string | null,
+): { readonly candidates: readonly string[]; readonly outside: boolean } {
+  // Codex round-2: normalize lexically FIRST so `lib/../../x` is seen as the traversal it is, and treat a
+  // Windows-drive path (`C:/…`) on a POSIX host as outside the package (counted, said) rather than as a
+  // package-relative name that silently matches nothing. Symlinked package dirs stay a named limit: the
+  // containment check is lexical, not realpath-based.
+  const p = posixNormalize(raw.replace(/\\/g, '/')).replace(/^(?:\.\/)+/, '');
+  if (p === '' || p === '.') return { candidates: [], outside: false };
+  if (/^[A-Za-z]:\//.test(p) && !isAbsolute(p)) return { candidates: [], outside: true };
+
+  if (isAbsolute(p)) {
+    const rel = relative(pkgDir, resolve(p)).split(sep).join('/');
+    return rel === '' || rel.startsWith('..') ? { candidates: [], outside: true } : { candidates: [rel], outside: false };
+  }
+
+  const candidates = new Set<string>();
+  if (p !== '..' && !p.startsWith('../')) candidates.add(p); // already package-relative, as given
+  if (repoTop !== null) {
+    const rel = relative(pkgDir, resolve(repoTop, p)).split(sep).join('/');
+    if (rel !== '' && !rel.startsWith('..')) candidates.add(rel);
+  }
+  return candidates.size > 0 ? { candidates: [...candidates], outside: false } : { candidates: [], outside: true };
+}
+
 function cmdMutationGate(
   options: Map<string, string>,
   flags: Set<string>,
@@ -12988,7 +13114,9 @@ function cmdMutationGate(
 
   let entries: readonly MutationRegistryEntry[] = parsed.registry.entries;
   let entryResults: readonly MutationEntryResult[] = parsed.entryResults;
+  const totalRegistryEntries = entries.length;
   const only = options.get('only');
+  let onlyIds: Set<string> | null = null;
   if (only !== undefined) {
     const ids = only.split(',').map((s) => s.trim()).filter(Boolean);
     const known = new Set([
@@ -12997,16 +13125,138 @@ function cmdMutationGate(
     ]);
     const unknown = ids.filter((id) => !known.has(id));
     if (unknown.length > 0) return fail(`--only names unknown entry id(s): ${unknown.join(', ')}`);
+    onlyIds = new Set(ids);
     entries = entries.filter((e) => ids.includes(e.id));
     entryResults = entryResults.filter((result) => ids.includes(result.id));
   }
 
+  // Feature qe-step-gate-scoped-to-feature (FR-1/FR-2/FR-3): scope the gate to the files a FEATURE
+  // actually touched and/or entries added since a base ref, instead of the whole registry — MEASURED
+  // 2026-09-12, 358 entries on this repo's core package ran 30-40 minutes and hit the timeout wall,
+  // INCONCLUSIVE every time, though a feature owns only its own touched files. `--touched` and
+  // `--added-since` UNION (a file changed by the feature OR an entry it newly added is in scope);
+  // that union then INTERSECTS with `--only` when both are given, same algebra as an ordinary filter
+  // chain. Both selectors are computed against the FULL (pre-`--only`) registry so their reported
+  // counts describe what THEY matched, independent of any `--only` narrowing applied on top.
+  const touchedRaw = options.get('touched');
+  const addedSinceRaw = options.get('added-since');
+  let selectionMeta: {
+    readonly selected: number;
+    readonly total: number;
+    readonly touched: readonly string[] | null;
+    readonly addedSince: readonly string[] | null;
+    readonly base: string | null;
+    readonly baseAbsent: boolean;
+    readonly outsidePackage: number;
+  } | null = null;
+  if (touchedRaw !== undefined || addedSinceRaw !== undefined) {
+    let repoTop: string | null = null;
+    try { repoTop = execSync('git rev-parse --show-toplevel', { cwd: pkgDir, stdio: 'pipe', encoding: 'utf-8' }).trim() || null; } catch { /* not in a git repo */ }
+
+    const touchedIds = new Set<string>();
+    let outsidePackageCount = 0;
+    if (touchedRaw !== undefined) {
+      const touchedPaths = touchedRaw.split(',').map((s) => s.trim()).filter(Boolean);
+      const normalizedCandidates = new Set<string>();
+      for (const raw of touchedPaths) {
+        const { candidates, outside } = normalizeTouchedPath(raw, pkgDir, repoTop);
+        if (outside) outsidePackageCount++;
+        for (const c of candidates) normalizedCandidates.add(c);
+      }
+      for (const entry of parsed.registry.entries) {
+        if (normalizedCandidates.has(entry.file)) touchedIds.add(entry.id);
+      }
+    }
+
+    const addedSinceIds = new Set<string>();
+    let baseAbsentMessage: string | null = null;
+    if (addedSinceRaw !== undefined) {
+      if (repoTop === null) return fail(`--added-since requires ${pkgDir} to be inside a git repository`);
+      try {
+        execFileSync('git', ['rev-parse', '--verify', '--quiet', `${addedSinceRaw}^{commit}`], { cwd: repoTop, stdio: 'pipe' });
+      } catch {
+        return fail(`--added-since names an unknown git ref: ${addedSinceRaw}`);
+      }
+      const registryRelPath = relative(repoTop, registryPath).split(sep).join('/');
+      let baseRegistry: MutationRegistry | null = null;
+      // Fix-round 1 (AM-3): only a genuinely ABSENT registry at that ref means "all entries are
+      // new". Any OTHER `git show` failure (a bad path that isn't a missing-registry case, git
+      // itself missing, a timeout) is a usage error, and a registry that parses to invalid JSON /
+      // an invalid registry shape at that ref is a distinct usage error too — collapsing all three
+      // into "absent" used to hide real failures behind a silently-too-generous selection.
+      try {
+        // stdio: registry-absent-at-ref is an EXPECTED outcome (git's own "fatal: path … does not
+        // exist" on stderr would otherwise leak to the terminal by node's default inherit-stderr
+        // behaviour) — pipe it into the caught error instead of printing it at the user.
+        const baseText = execFileSync('git', ['show', `${addedSinceRaw}:${registryRelPath}`], { cwd: repoTop, encoding: 'utf-8', env: { ...process.env, LC_ALL: 'C', LANG: 'C' }, maxBuffer: 16 * 1024 * 1024, stdio: ['ignore', 'pipe', 'pipe'] });
+        const baseParsed = parseMutationRegistry(baseText);
+        if (baseParsed.registry === null) {
+          return fail(`base registry at ${addedSinceRaw} is not a valid registry: ${baseParsed.errors.join('; ')}`);
+        }
+        baseRegistry = baseParsed.registry;
+      } catch (e) {
+        const stderr = typeof (e as { stderr?: unknown })?.stderr === 'string'
+          ? (e as { stderr: string }).stderr
+          : String((e as Error)?.message ?? e);
+        if (/does not exist in|exists on disk, but not in|Path .* does not exist/i.test(stderr)) {
+          baseRegistry = null; // registry absent at that ref → every current entry counts as added
+          baseAbsentMessage = `base registry absent at ${addedSinceRaw} — all ${totalRegistryEntries} entries count as added`;
+        } else {
+          return fail(`git show ${addedSinceRaw}:${registryRelPath} failed: ${stderr.trim()}`);
+        }
+      }
+      if (baseAbsentMessage !== null && !json) write(`mutation-gate: ${baseAbsentMessage}`);
+      for (const id of registryEntriesAddedSince(baseRegistry, parsed.registry)) addedSinceIds.add(id);
+    }
+
+    let unionIds = new Set<string>([...touchedIds, ...addedSinceIds]);
+    if (onlyIds !== null) {
+      const only2 = onlyIds;
+      unionIds = new Set([...unionIds].filter((id) => only2.has(id)));
+    }
+    const selectorParts: string[] = [];
+    if (touchedRaw !== undefined) selectorParts.push(`touched: ${touchedIds.size}${outsidePackageCount > 0 ? ` (${outsidePackageCount} outside package)` : ''}`);
+    if (addedSinceRaw !== undefined) selectorParts.push(`added-since ${addedSinceRaw}: ${addedSinceIds.size}`);
+    if (!json) write(`mutation-gate: selected ${unionIds.size} of ${totalRegistryEntries} entries (${selectorParts.join('; ')})`);
+    entries = entries.filter((e) => unionIds.has(e.id));
+    entryResults = entryResults.filter((result) => unionIds.has(result.id));
+
+    // AM-4: every scoped run — empty or not — carries a machine-readable `selection` object in the
+    // JSON contract, not just the empty-selection early return.
+    selectionMeta = {
+      selected: unionIds.size,
+      total: totalRegistryEntries,
+      touched: touchedRaw !== undefined ? [...touchedIds].sort() : null,
+      addedSince: addedSinceRaw !== undefined ? [...addedSinceIds].sort() : null,
+      base: addedSinceRaw ?? null,
+      baseAbsent: baseAbsentMessage !== null,
+      outsidePackage: outsidePackageCount,
+    };
+
+    if (unionIds.size === 0) {
+      const msg = `0 entries match ${selectorParts.join(', ')} — nothing to run`;
+      if (json) {
+        write(JSON.stringify({
+          packageDir: pkgDir,
+          registryPath,
+          selection: selectionMeta,
+          results: [],
+          summary: summarizeMutationResults([]),
+          exitCode: 0,
+        }, null, 2));
+      } else {
+        write(`mutation-gate: ${msg}`);
+      }
+      return 0;
+    }
+  }
+
   if (entries.length === 0) {
     const scope = only === undefined ? 'registry' : 'selected registry entries';
     const error = `${scope} has no runnable entries after validation — nothing can be run; the registry is unusable`;
     const summary = summarizeMutationResults(entryResults);
     if (json) {
-      write(JSON.stringify({ error, registryPath, results: entryResults, summary, exitCode: 2 }, null, 2));
+      write(JSON.stringify({ error, registryPath, ...(selectionMeta !== null ? { selection: selectionMeta } : {}), results: entryResults, summary, exitCode: 2 }, null, 2));
     } else {
       write(`dz mutation-gate: ${error}`);
       for (const result of entryResults) {
@@ -13018,7 +13268,7 @@ function cmdMutationGate(
 
   const testCmdRaw = options.get('test-cmd') ?? parsed.registry.testCommand ?? 'npm test';
   if (/[\0\n\r]/.test(testCmdRaw)) return fail('--test-cmd may not contain NUL or newline characters');
-  const testCmd = testCmdRaw;
+  let testCmd = testCmdRaw;
   const excludedSelfChecks = REGISTRY_SELFCHECK_TESTS.filter((testFile) =>
     entries.some((entry) => buildMutationTestCommand(testCmd, entry).excluded.includes(testFile)),
   );
@@ -13026,8 +13276,88 @@ function cmdMutationGate(
     write(`mutation-gate: self-check excluded from mutant runs: ${excludedSelfChecks.join(', ') || '(none)'}`);
   }
 
-  const timeoutOpt = Number(options.get('timeout') ?? '300000');
-  const timeout = Number.isFinite(timeoutOpt) && timeoutOpt > 0 ? timeoutOpt : 300000;
+  // mutation-gate-timeout-verdict FR-3/FR-4: precedence is the `--timeout` flag > the registry's
+  // own `timeoutMs` field > the 300000ms default. A package whose real baseline run is longer than
+  // the default (this repo's core package, MEASURED ≈5-8 min) declares its floor in the registry so
+  // a bare `dz mutation-gate` — no flag — still succeeds (AC-5).
+  const timeoutFlagRaw = options.get('timeout');
+  let timeout: number;
+  let timeoutSource: 'flag' | 'registry' | 'default';
+  if (timeoutFlagRaw !== undefined) {
+    const timeoutOpt = Number(timeoutFlagRaw);
+    if (Number.isFinite(timeoutOpt) && timeoutOpt > 0) {
+      timeout = timeoutOpt;
+      timeoutSource = 'flag';
+    } else {
+      timeout = 300000;
+      timeoutSource = 'default';
+    }
+  } else if (parsed.registry.timeoutMs !== undefined) {
+    timeout = parsed.registry.timeoutMs;
+    timeoutSource = 'registry';
+  } else {
+    timeout = 300000;
+    timeoutSource = 'default';
+  }
+  if (!json) write(`mutation-gate: timeout: ${timeout} ms (${timeoutSource})`);
+
+  // mutation-gate-baseline-honesty FR-2/FR-3: precedence is the `--max-workers` flag > the
+  // registry's own `maxWorkers` field > `min(4, max(1, floor(cpus/2)))`. Baseline and mutant runs
+  // spawn the package's FULL testCommand at vitest's DEFAULT worker count (= cpu cores) unless
+  // capped — MEASURED: under embedding-daemon tests (0.7-3.5 GB/process) this repo's core package
+  // hit load 62-358 and 0.4-1.8 GB free on an 8-core/16GB box, killing three full overnight runs
+  // (0bb74d66); the same suite at `--maxWorkers=2` passed 6909/6909.
+  const maxWorkersFlagRaw = options.get('max-workers');
+  const defaultMaxWorkers = Math.min(4, Math.max(1, Math.floor(cpus().length / 2)));
+  let maxWorkers: number;
+  let maxWorkersSource: 'flag' | 'registry' | 'default';
+  if (maxWorkersFlagRaw !== undefined) {
+    // fix-round 1, AM-1: an invalid `--max-workers` value (0, negative, fractional, `NaN`,
+    // non-numeric) is a USAGE ERROR (exit 2) — mirroring the `--only` unknown-id fail() style —
+    // never a silent fallback to the default. A silent fallback would make a typo'd flag run
+    // uncapped-by-mistake while LOOKING capped (the source line still says "(default)").
+    const maxWorkersOpt = Number(maxWorkersFlagRaw);
+    if (!Number.isInteger(maxWorkersOpt) || maxWorkersOpt < 1) {
+      return fail(`--max-workers must be a positive integer, got '${maxWorkersFlagRaw}'`);
+    }
+    maxWorkers = maxWorkersOpt;
+    maxWorkersSource = 'flag';
+  } else if (parsed.registry.maxWorkers !== undefined) {
+    maxWorkers = parsed.registry.maxWorkers;
+    maxWorkersSource = 'registry';
+  } else {
+    maxWorkers = defaultMaxWorkers;
+    maxWorkersSource = 'default';
+  }
+  // FR-3: inject the ceiling into the command ONLY when it is (detectably) a vitest run and does
+  // not already name the flag itself — an arbitrary testCommand cannot be assumed to accept
+  // `--maxWorkers`. VITEST_MAX_WORKERS is set in the env unconditionally (below, at spawn time)
+  // regardless of this detection, so a vitest command reached indirectly (e.g. through a package
+  // script) is still capped.
+  // fix-round 1, AM-3: detection AND injection are scoped to the VITEST SEGMENT — from the first
+  // `vitest run` token to the next `&&`/`||`/`;`/`|` (or end of string) — and the flag lands right
+  // after `vitest run`, never appended to the tail of a whole (possibly compound) command. A
+  // raw-substring append over the FULL command turned `vitest run … && cleanup` into
+  // `vitest run … && cleanup --maxWorkers=2` (silently handed to `cleanup`, not vitest), and the
+  // existing-flag check could be suppressed by an unrelated `--maxWorkers` substring living outside
+  // the vitest segment entirely (e.g. inside `cleanup`'s own args, or before `vitest run` in the
+  // same command).
+  const vitestRunIdx = testCmd.indexOf('vitest run');
+  const isVitestCommand = vitestRunIdx !== -1;
+  if (isVitestCommand) {
+    const tailFromRun = testCmd.slice(vitestRunIdx);
+    const terminator = /&&|\|\||;|\|/.exec(tailFromRun);
+    const vitestSegment = terminator !== null ? tailFromRun.slice(0, terminator.index) : tailFromRun;
+    if (!vitestSegment.includes('--maxWorkers')) {
+      const insertAt = vitestRunIdx + 'vitest run'.length;
+      testCmd = `${testCmd.slice(0, insertAt)} --maxWorkers=${maxWorkers}${testCmd.slice(insertAt)}`;
+    }
+  }
+  if (!json) {
+    write(isVitestCommand
+      ? `mutation-gate: workers: ${maxWorkers} (${maxWorkersSource})`
+      : 'mutation-gate: workers: n/a — test command is not vitest');
+  }
 
   // Route-b guard mode: `per-entry` (default, strongest — each red entry re-baselines the restored
   // tree, so a flaky neighbour flips THAT entry to INCONCLUSIVE) or `final` (cheap — one re-run at
@@ -13108,22 +13438,29 @@ function cmdMutationGate(
       phase: 'baseline' | 'mutation' | 'rebaseline' | 'final-rebaseline',
       entryId?: string,
     ): MutationGateRunnerObservation => {
+      // FR-3: VITEST_MAX_WORKERS is set in any case — regardless of whether the command was
+      // recognised as vitest and got the `--maxWorkers=<n>` flag injected — so a vitest command
+      // reached indirectly (a wrapper script) is still capped.
+      const extraEnv: Readonly<Record<string, string>> = { VITEST_MAX_WORKERS: String(maxWorkers) };
       if (injectedRunner !== undefined) {
         return injectedRunner(suiteCommand, {
           cwd: copyDir,
           timeoutMs: timeout,
           phase,
+          env: extraEnv,
           ...(entryId !== undefined ? { entryId } : {}),
         });
       }
+      const startedAt = performance.now();
       const run = spawnSync(suiteCommand, {
         cwd: copyDir,
         shell: true,
         encoding: 'utf-8',
         timeout,
         maxBuffer: 64 * 1024 * 1024,
-        env: { ...process.env, FORCE_COLOR: '0' },
+        env: { ...process.env, FORCE_COLOR: '0', ...extraEnv },
       });
+      const elapsedMs = Math.round(performance.now() - startedAt);
       const errorCode = run.error && 'code' in run.error && typeof run.error.code === 'string'
         ? run.error.code
         : undefined;
@@ -13134,10 +13471,28 @@ function cmdMutationGate(
         throw run.error;
       }
       const signal = typeof run.signal === 'string' ? run.signal : undefined;
+      // mutation-gate-timeout-verdict FR-1/FR-2: a genuine ETIMEDOUT must NEVER be read as a real
+      // suite verdict, even when the killed child intercepted the kill signal and exited with its
+      // OWN status (e.g. a SIGTERM handler calling `process.exit(1)`) — MEASURED: node still sets
+      // `run.error.code === 'ETIMEDOUT'` in that case, but a numeric `run.status` used to win the
+      // `typeof run.status !== 'number'` check below, so the timeout was silently reported as
+      // "baseline suite RED (exit 1)", indistinguishable from a real red suite. ETIMEDOUT now short
+      // -circuits to `exitCode: null` unconditionally, before that check runs.
+      if (errorCode === 'ETIMEDOUT') {
+        // Codex round-1 (2026-09-14): report BOTH facts when both exist — a trapped SIGTERM that
+        // exits 1 shows `child exit 1; signal SIGTERM`, a plain kill shows `no exit code; signal …`.
+        const exitPart = typeof run.status === 'number' ? `child exit ${run.status}` : 'child produced no exit code';
+        const childExit = signal === undefined ? exitPart : `${exitPart}; signal ${signal}`;
+        const suggestedMs = Math.max(timeout + 1, Math.ceil(elapsedMs * 2));
+        return {
+          exitCode: null,
+          output: `${String(run.stdout ?? '')}\n${String(run.stderr ?? '')}`,
+          failureReason: `timeout after ${timeout}ms (elapsed ${elapsedMs}ms); ${childExit}; try --timeout ${suggestedMs} or the registry's timeoutMs field`,
+        };
+      }
       let failureReason: string | undefined;
       if (typeof run.status !== 'number') {
-        if (errorCode === 'ETIMEDOUT') failureReason = `timeout after ${timeout}ms${signal === undefined ? '' : `; signal=${signal}`}`;
-        else if (errorCode === 'ENOBUFS') failureReason = 'maxBuffer exceeded (ENOBUFS; 67108864-byte output ceiling)';
+        if (errorCode === 'ENOBUFS') failureReason = 'maxBuffer exceeded (ENOBUFS; 67108864-byte output ceiling)';
         else if (signal !== undefined) failureReason = `child killed by signal ${signal}`;
         else if (errorCode !== undefined) failureReason = `spawn failure code ${errorCode}`;
         else failureReason = 'spawn failure with no error code or signal';
@@ -13389,7 +13744,7 @@ function cmdMutationGate(
 
   const exitCode = mutationGateExitCode(results, baseline.ok);
   if (json) {
-    write(JSON.stringify({ packageDir: pkgDir, registryPath, testCommand: testCmd, rebaselineMode, baseline, results, summary: summarizeMutationResults(results), warnings, internalRetries, exitCode }, null, 2));
+    write(JSON.stringify({ packageDir: pkgDir, registryPath, testCommand: testCmd, rebaselineMode, baseline, results, summary: summarizeMutationResults(results), warnings, internalRetries, ...(selectionMeta !== null ? { selection: selectionMeta } : {}), exitCode }, null, 2));
     return exitCode;
   }
   write(renderMutationReport(results, baseline, pkgDir));
@@ -20541,7 +20896,7 @@ export async function runCli(argv: string[], io: CliIo = {}): Promise<number> {
       case 'release':
         return cmdRelease(options, flags, cwd, write, io.releaseRunner);
       case 'parity':
-        return cmdParity(options, flags, write, writeErr, cwd);
+        return await cmdParity(options, flags, write, writeErr, cwd);
       case 'registry':
         return cmdRegistry(options, cwd, write);
       case 'benchmark':

package/src/known-flags.ts

@@ -10,6 +10,7 @@
  * See harness-core/src/cli-flag-notice.ts for the full reasoning and the honest limit.
  */
 export const KNOWN_CLI_FLAGS: readonly string[] = [
+  'added-since',
   'affected',
   'all',
   'allow-cold-start',
@@ -162,6 +163,7 @@ export const KNOWN_CLI_FLAGS: readonly string[] = [
   'max',
   'max-per-day',
   'max-wall-clock',
+  'max-workers',
   'memory',
   'mock',
   'mode',
@@ -239,6 +241,10 @@ export const KNOWN_CLI_FLAGS: readonly string[] = [
   'pubkey',
   'publish',
   'quarter',
+  // Not a dz flag: `git rev-parse --verify --quiet` is a git argument this CLI passes through
+  // (mutation-gate --added-since ref validation) — same pass-through class as the git-diff volume
+  // counters noted above.
+  'quiet',
   'reason',
   'rebaseline',
   'recalled',
@@ -324,6 +330,7 @@ export const KNOWN_CLI_FLAGS: readonly string[] = [
   'topic',
   'topics',
   'tokens',
+  'touched',
   'transcript',
   'type',
   'untracked-files', // git status argument