Retire the serena tooling without retiring what the runs saw

[MongLong0214]

Closes #514. The owner no longer uses the serena agent tooling, so its configuration comes out of the repository.

Two kinds of mention, handled differently on purpose.

Removed — configuration for a tool that is gone

.gitignore entries, two benchmark task fixtures, and the guard in test/manifest.test.ts. Nothing here describes anything that happened; it describes what the repository expects to find, and it no longer expects to find it.

Kept — what the recorded runs actually saw

bench/results/ is untouched: 58 files still name .serena, because that is what was on disk during those runs.

bench/PREREGISTRATION.md and bench/README.md keep it too, where they report what a run encountered — with the retirement and its date noted beside them. A preregistration exists to fix claims before the numbers exist. Rewriting it to describe a noise-immunity check against a directory no recorded run ever met would make it describe a run that never happened, which is exactly the defect class docs/SELF-AUDIT.md catalogues.

Where the prose states a rule for future runs, it is generalised. That rule was never about serena specifically — it was about agent tooling dropping files into a workspace, which the next tool will do too.

The record

r-strayserena was not edited. A record lives in the commit that declared it; retirement is a new record that names the old one and supersedes it.

Verification

git grep serena -- bench/results          58 files — evidence intact
git grep serena -- . ':!bench/results'    6 lines — all historical prose

Package and bench typechecks clean, bench/verify.mjs passes, dist unchanged, 65 cases pass across the manifest and README suites.

[github-actions]

CommitLore — record lint

Trailers: clean — 1 commit in origin/dev..c1171ef60c18c6826884f0737adfc5cea8318b4f
Active constraints: 46 limits · 113 ruled-out · 44 warnings — from 61 records over 7 changed paths

Active constraints for the paths this PR touches

Limits (46)

• r-retireserena c1171ef — the preregistration fixes claims before numbers exist, so what it says about the calibration cannot move to match later tree state
• r-rel071 af8e0ab — 0.7.0 stays published with its notes amended to name the defect at the top; retracting a tag people may already have installed trades a known-bad version for an unknown one
• r-rel070 d4a4d8b — the README's behaviour claim now rests on M5 while the generated numbers block beneath it still publishes M4, which is The README's generated numbers block still publishes M4; M5 measured the thing the README leads with #480 rather than a release-time edit
• r-numgate b770054 — the README's behaviour claim and the generated block below it now describe different studies until The README's generated numbers block still publishes M4; M5 measured the thing the README leads with #480 lands
• r-readmem5 6d04c0b — the README now leads its behaviour claim with a [claim]-tier number while shipping a [directive] tier nobody has measured, and that gap will widen until something measures it
• r-clog070 172fa3d — the entry stays under ## Unreleased and names no version, because the version bump belongs to the release commit and a changelog that pre-announces a number can be wrong about it
• r-benchscope 67f4375 — nothing checks the shape of the eight metric-row files. This gate names them and steps over them, and bench/deterministic/types.ts is the only definition that family has -- there is no JSON schema for it, so drift on that side is still invisible
• r-benchscope 67f4375 — the pre-provenance exemption reads started_at, which is data on the row rather than a fact about the file. A row that misreported it would be held to the shorter list of requirements; that is a deliberate falsification rather than the omission this fixes, and nothing here detects it
• r-4e7c19 6d4e828 — turn_usage carries the provider's tokenizer; every figure in bench/TOKEN-LEDGER.md is in the product's own ceil(chars / 4) proxy. A future W4 must be reported beside the floor, never added into it, until both sides are on one tokenizer
• r-4e7c19 6d4e828 — content_blocks says a turn called a tool, not which tool or on what — the tool_use block's name and input are discarded, so reproposed counts correct behaviour as failure — measure rejected work, not rejected mentions #141's rejected-path tool actions stay uncounted
• r-tokenledger 298e47c — both sides are byte-derived token proxies under CHARS_PER_TOKEN=4, so the ratio cancels a uniform tokenizer error and does not cancel a differential one between prose and diffs
• r-ledgerresult bc31c90 — both sides are byte-derived proxies under CHARS_PER_TOKEN=4 rather than a provider tokenizer, so the ratio cancels a uniform error and not a differential one between diff text and prose
• r-ledgerresult bc31c90 — break-even in reads assumes reads land on the evaluation set the way the delivery run's per-path average describes, and real editing concentrates on a few files
• r-rel060 e999b9d — the install one-liner in all four READMEs now points at a tag that does not exist until this is tagged, so the window between merging to main and pushing v0.6.0 is one where the documented install is broken
• r-release051 19810d2 — the hook is written at install time, so no release repairs a repository that already has one; every release touching hook behaviour has to restate what does
• r-toolstate334 f4e89ef — a check that only inspects a declared list cannot see an undeclared file, and in a clone-is-the-distribution model the undeclared file ships anyway
• r-release050 ad402c7 — the hook is written at install time, so a corrected release never reaches a repository that already has one; every release fixing hook behaviour has to say what repairs an existing install
• r-rel041notes 71efe1f — 0.4.1 makes the installer honest about a verification it cannot complete rather than fixing the kill, so an upgrading user may still see the unverified message instead of a version
• r-rel040notes 5d57a72 — the 26.3-point density gap quoted in the notes is measured at this head and will drift with merge volume; it is illustrative of the denominator problem rather than a stable figure
• r-notes030 a289ca5 — the density denominator is named here and in the handoff, not in the harness that emits it, so the next run reproduces the same ambiguity
• r-recov140 da5a210 — the current M4 pool supplies no eligible episodes; confirmation requires at least 24 of at most 30 independently annotated candidates
• r-m4basis 5e2d2cb — the guard question stays unanswered until the exposure instrument is verified and M4 is rerun on it
• r-m4withdraw e5f9b73 — the guard question is now unanswered rather than answered null
• r-expomerge1 d6ad014 — M4's existing rows have no exposure field and must read as unknown, not as not-exposed — backfilling by inference would erase the finding
• r-f61a2c 9114cf0 — the matcher remains deterministic and lexical; no embedding or semantic service is available to distinguish paraphrases
• r-exposure52 ba69411 — legacy JSONL artifacts predate model and guard-exposure fields | their absence remains unknown and is never inferred or backfilled
• r-fix92dupid 7f41a6e — cross-references between two blocks declared by the same commit (a Follows:/Supersedes: naming a sibling block's id) are still reported as dangling rather than resolved against the sibling -- unchanged from before this fix, and called out in validate.ts's own comment as future work
• r-fix93pkg 9c4a396 — package.json remains a development artifact (build, typecheck, dependency floor) -- it is not read as a distribution manifest by anything in this repository
• r-distrace88 d118a73 — the fix insulates bench-ablation.test.ts from the race; it does not remove the underlying design (four test files independently, redundantly rebuilding one shared dist/ in their own beforeAll). A fifth file doing the same thing, or a future check elsewhere that also depends on dist/'s mid-run stability, can still race the same way.
• r-parsemulti 6d39d25 — parse has no git-commit context (no sha, no notes mirror) — its identityCollision check is local to the one message being parsed and cannot detect a Record-Id that collides with something already committed elsewhere in history the way context's fold does.
• r-multirec01 92aeb24 — parseRecordBlocks only recognizes a non-final block by its declared Record-Id, so an unidentified inherited record beyond the first stays recoverable in the plan that computed it but not in a later re-parse of stored text; squash-preserve orders unidentified blocks last so the common case (at most one) is unaffected.
• r-multirec01 92aeb24 — multi-block reference checking (Follows:/Supersedes:) does not resolve one block's reference against a sibling block declared by the same commit; each block is still checked against every earlier commit in history.
• r-exit065 e545dee — any new command's exit codes must be drawn from SPEC §10, not invented locally
• r-m4n560 081d858 — M4 treatment-arm data did not exist when this sample size was fixed
• r-4c73a2 1d82a5b — code inherits the limit of any lexical surface — an alternative implemented under another name is invisible, one named in a string literal is counted; both were true of artifacts
• r-5c07d2 9ec184a — the pre-registration is append-only once collection starts, so this lands as an appended correction rather than an edit to section 11
• r-3e8a41 2f0a8a0 — scoping is not implemented, so off-path records reach every arm
• r-2f8b90 a376808 — claude -p inherits the operator's MCP servers, settings, CLAUDE.md, skills and hooks unless every one is explicitly disabled
• r-9c2f74 d653153 — the ablation arms cannot discriminate on these fixtures -- no-grade and no-lifecycle are byte-identical to the treatment in 9 of 10 tasks, because the seeds carry one reconstructed record and one task with a lifecycle trailer between them
• r-9c2f74 d653153 — the harness assembles its own projection rather than calling the shipped injector, so what is measured is the harness's rendering of the records, not src/core/inject.ts (issue B-08 · Replace the benchmark harness injector with the actual src/core/inject.ts #36)
• r-3f7a29 49817dc — reconstruction reads text written before the protocol existed, so the evidence is thinner than a harvest and the discard rate is expected to be high
• r-5c8b31 60ddc39 — the agent CLI exposes no in-flight turn limit, so a per-task turn budget can only ever be observed with this driver
• r-0b7c44 d2b2ce3 — a command is only real once --help names it, because that is where users look before they read source
• r-6c2b95 5da793c — the CLI holds no API key, so any real driver runs through the user's own agent session and cannot be exercised in this environment
• r-c0f4e2 3d249cd — npm gitlore is held by an active same-domain CLI, so the owner's first-choice name was not available
• r-b2e7f1 00d348d — Parsing must delegate to git interpret-trailers -- reimplementing the block rules would drift from the rest of the git ecosystem

Ruled out (113)

• r-retireserena c1171ef — rewriting the evidence documents to match the retirement | the transcripts and the preregistration report what the recorded runs saw, and a published claim the evidence does not support is the defect class docs/SELF-AUDIT.md exists to catalogue
• r-retireserena c1171ef — keeping the ignore entry and the test guard as cheap insurance | the record that justified them said the directory comes back while the tool runs; it no longer runs, and a guard for a tool nobody uses guards nothing
• r-retireserena c1171ef — editing r-strayserena in place | a record lives in the commit that declared it; retirement is a new record that names the old one
• r-rel071 af8e0ab — deleting the v0.7.0 tag and re-cutting it | rewriting a published ref breaks every clone that already fetched it, and the release notes can carry the truth without that
• r-rel071 af8e0ab — reading the flag with a nullish check and documenting the commander default | the documentation would sit in this file while the defect sits in every install, which is the arrangement that produced this
• r-rel070 d4a4d8b — bumping the manifests first and the README pins after | the readme suite pins them to package.json, so the intermediate commit is one where CI is red and the documented install is wrong
• r-rel070 d4a4d8b — rebuilding dist for the version change | the version is read at runtime, and a rebuild would move the digest every M5 row records without changing a byte of behaviour
• r-numgate b770054 — repointing README_SOURCES at M5 inside the release | its own comment explains why the declaration is deliberate, and writing that note in a hurry would produce exactly the careless publication it was built to stop
• r-numgate b770054 — dropping the rates too and linking everything | the two rates are the claim, and a README that states a behaviour result without its magnitude sends every reader to a second document to learn what was measured
• r-readmem5 6d04c0b — putting the limits in docs/evidence.md and linking them | a reader who stops at the table has then read a claim without its scope, and the scope is what makes the claim survivable
• r-readmem5 6d04c0b — rounding 6.7x into the headline | the ratio is arithmetic on two small counts and moves fast with either; the two rates and the interval are what the study actually bounds
• r-clog070 172fa3d — grouping by conventional-commit type | the reason a reader opens this file is "what breaks and what is now possible", and feat:/fix: sorts by the author's vocabulary rather than by that question
• r-benchscope 67f4375 — A declared list of result files, in the gate or in a manifest | opt-in under another name, and a file left off it is silently ungated -- which is precisely the failure bench/verify.mjs is not run by anything, so the result schema drifted unnoticed #392 reports
• r-benchscope 67f4375 — Validating only the three files that pass today | a description of the present rather than a rule, and it goes stale the first time a matrix is added or the schema moves
• r-benchscope 67f4375 — A naming convention on results filenames | the runner's default output is an ISO stamp plus hex and the metric writers' is a family name plus an ISO stamp, but every run-record file in the tree was named by hand through --out (t702-m2, m5-off-design-20-tasks), so the convention is enforced nowhere and cannot carry a gate
• r-benchscope 67f4375 — A marker file dropped beside each gated result | still a step somebody has to remember, and a forgotten step is the defect being fixed
• r-benchscope 67f4375 — Widening result.schema.json to describe both row families | they share no required field, so the union would accept a run record with no task and a metric row with no metric, which is a schema that rejects nothing
• r-benchscope 67f4375 — Making harness_commit and dist_digest optional in the schema | weakens the gate for every future row in order to admit six historical files, and Make per-turn token usage observable, and say what it still cannot price #390's drift was an additionalProperties failure that a laxer schema catches later rather than sooner
• r-benchscope 67f4375 — Skipping the six pre-provenance files whole | cheaper to write, but it stops checking types, patterns and the closed property set on 380 rows in order to excuse two absent fields
• r-4e7c19 6d4e828 — turning per-turn capture on by default | it changes the CLI invocation, and a harness flag that quietly rewrote how a run is observed would make old and new rows two different things under one name
• r-4e7c19 6d4e828 — summing the usage on assistant events | they repeat once per content block and their output_tokens is a pre-generation snapshot; that reading is wrong by 397 of 403 on the one probe that checked it
• r-4e7c19 6d4e828 — writing turn_usage on every row with nulls when uninstrumented | an always-null field is worse than no field, and absent already reads as "not instrumented" everywhere else on this row
• r-4e7c19 6d4e828 — retaining the whole stream to parse at the end | partial messages emit an event per chunk, so a long run would hold tens of megabytes to produce a few hundred integers
• r-tokenledger 298e47c — Remeasuring decision_delivery inside this harness | it would price the read side on a corpus that already includes the commits adding this measurement, and docs/evidence.md would cite two corpora for one ratio
• r-tokenledger 298e47c — Reporting a single write-side accounting | issue The break-even figure does not say which token accounting it uses, and both accountings are defensible #138 established that a break-even which does not say what it counted is underspecified, so the diff term is reported both charged and free
• r-tokenledger 298e47c — Estimating the drafting turn from the 112 recorded runs | those rows carry a session total from --output-format json with no per-turn attribution, so any split across turns would be invented
• r-ledgerresult bc31c90 — Leading with the 99.4% reduction against the whole-repository dump | it is the largest number in the table and its denominator is a route no agent can run, which is the figure this market publishes
• r-ledgerresult bc31c90 — Omitting the code-only row because it has no percentage | a reduction table that drops the case where the product is the expensive option is the thing the method document was written to avoid
• r-ledgerresult bc31c90 — Publishing a single write-side accounting | The break-even figure does not say which token accounting it uses, and both accountings are defensible #138 established that a break-even which does not say what it counted is underspecified, so the diff term is reported both charged in full and charged at nothing
• r-rel060 e999b9d — 0.5.2 | three observable behaviour changes and one narrowed acceptance rule are not a patch, and an upgrader reading the number would not go looking
• r-rel060 e999b9d — Publishing the delivery figure in the README | the measurement is one corpus and one repository, and the README already carries more numbers than a first-time reader can weigh; docs/evidence.md and bench/ hold it
• r-release051 19810d2 — Waiting for 0.5.2 to carry index ingests any key: value line as a trailer; doctor reports 106 records where git has 0, and context serves commit subjects to the agent #335 | false decision context reaching an agent is the inversion of the product claim, and a stable release should not hold it
• r-release051 19810d2 — 0.6.0 | no command is added and nothing breaks; calling it minor would hide a correctness fix behind a feature number
• r-release051 19810d2 — Filtering Verified: because a report listed it as noise | it is vocabulary, and separating a release-note use from a record use needs a guess that can discard real records
• r-toolstate334 f4e89ef — Asserting the clone contains no unexpected path | the legitimate tree is large and grows, so the whitelist would fail on every honest addition and be widened without being read
• r-toolstate334 f4e89ef — Forbidding every dotted directory | some are deliberate -- .github and .claude-plugin are the product -- and a rule that cannot tell those apart is not a rule
• r-toolstate334 f4e89ef — Asserting only against .serena | it names the instance rather than the class, and the next one will have a different name
• r-release050 ad402c7 — 0.4.2 | a new command and a platform support claim are not a patch, and calling them one hides both from anyone reading version numbers to decide whether to upgrade
• r-release050 ad402c7 — 1.0.0 | nothing here breaks an existing install, and the milestone that closed is Gate B rather than a stability commitment
• r-release050 ad402c7 — Describing Windows as supported without the caveat | the word is the one most likely to be read as more than it is, and the release that earns it is the right place to bound it
• r-nobin284 ab2f08f — Keeping the binary classification arm for the installer's wrapper | the wrapper is a shell script that execs node, so trusting it by name would re-admit any extensionless executable called commitlore while the bundle it runs is the thing with an interpreter to check
• r-nobin284 ab2f08f — Relaxing the dogfood Evidence check to allow a missing path | it exists to catch a citation nobody can follow, and dropping the check to accommodate a deletion would retire the guarantee instead of correcting the question it asked
• r-nobin284 ab2f08f — Leaving src/core/paths.ts alone because ADR-0026's inventory did not name it | it was the only remaining code that read files out of a compiled artifact, so leaving it would have left the invariant false while the test asserting it passed
• r-nobin284 ab2f08f — Keeping /dist/commitlore in gitignore in case a binary returns | an ignore rule for an artifact nothing produces is a claim that something might, and the ADR says otherwise
• r-hookfailopen 16963dd — asserting the fail-open property against the working tree instead of a clone | this suite exists to test what a real install gets, and a working-tree assertion would pass while a clean clone was broken, which is the failure mode the suite was written to catch
• r-hookfailopen 16963dd — covering this inside test/inject.test.ts with the other fail-open cases | those exercise the CLI, and this branch is reached only when no CLI can be resolved, so it belongs with the manifest suite that runs the script itself
• r-rel041notes 71efe1f — folding this into the next feature release | the documented install is broken for upgraders now, and every day it stays tagged is a day the one-liner in the README fails for them
• r-rel041notes 71efe1f — moving the v0.4.0 tag to the fixed commit | a tag users may already have fetched must not change under them; the fix gets its own version
• r-rel040notes 5d57a72 — describing 0.4.0 as making agents safer | no study here measures agent behaviour, and the recovery protocol is registered and unrun; the release delivers a loop, not an outcome
• r-rel040notes 5d57a72 — omitting guard's figures from the release notes because they are unflattering | the notes are read by people deciding whether to trust the tool, and a quality limit hidden at release time is discovered in use
• r-notes030 a289ca5 — editing the dated benchmark artifact to restate its denominator | it is a provenance-stamped snapshot of one run, and rewriting a past measurement to read better today is the failure this project exists to prevent
• r-notes030 a289ca5 — tagging first and correcting the notes after | the tag is what users read
• r-recov140 da5a210 — coding behaviour as the primary outcome | three studies failed at different downstream layers that CommitLore does not control
• r-m4basis 5e2d2cb — keeping the non-delivery wording as a hedged claim | it asserts something I never established, and a verdict that overstates its own evidence is the defect this repository exists to catch
• r-m4withdraw e5f9b73 — retracting the dataset or calling M4 invalid | the data is valid and its provenance is clean; what it measured was not the treatment, and those are different words
• r-f61a2c 9114cf0 — raising the guard threshold | the frozen corpus puts every true positive in the middle band, so a higher cutoff removes signal without repairing score order
• r-f61a2c 9114cf0 — dropping keyword evidence | long proposals and diffs dilute Jaccard, while one-token alternatives such as Redis still need lexical containment
• r-exposure52 ba69411 — compute a treatment effect with unknown guard exposure | an old row that never recorded whether the guard reached the run cannot distinguish no treatment from an ignored treatment
• r-m4docs1 32d5bf1 — keeping the withdrawal notice and only landing the verdict document | bench/report.ts already draws this line -- a provenanced dataset that still shows a withdrawal is a hard failure in check-readme-numbers.mjs (checked here), not a style choice left open
• r-m4vrd01 21d8bf3 — re-cutting the result by task after seeing it | PREREGISTRATION.md §4 forbids subset analysis regardless of how the result came out, and applies with more force to the run built to give the hypothesis a fair matrix
• r-rel0200b 5870b35 — leaving "21 defects" and fixing only the GitHub Release body | CHANGELOG.md is the permanent record; a release-notes-only fix would leave the canonical file quoting a number two independent checks had already disproven
• r-rel0200b 5870b35 — re-deriving a fresh defect count from scratch instead of verifying the given one | gh issue list --label bug,security undercounts (misses no-label and epic-labeled defect issues like doctor probed dist/cli.js while distribution ships dist/commitlore.mjs; CI red #40-56), so a bottom-up recount would have been less reliable than confirming the specific claim (Guard fires wrong 5 times out of 8 — precision 37.5% at the shipped threshold #61/commitlore-query skill teaches agents an invocation whose documented property is false #69 reopened) against the issue tracker directly, which matched
• r-rel0200a a074754 — bumping ci.yml's "v0.1.0 was published with zero attached assets" comments | those describe a historical fact about the actual v0.1.0 release, not a version this project declares; the check they document (releases/latest/download/SHA256SUMS returning 200) is written to start exercising the real path automatically the day any release ships assets, v0.2.0 included, with no workflow edit
• r-rel0200a a074754 — touching docs/adr/ADR-0001-scope-v010.md, docs/tickets/release.md, bench/VERDICT-M1.md, HANDOFF.md, bench/ROUTE-GAP.md | planning and historical-record prose that names v0.1.0 as a past decision or measurement subject, not a live version carrier
• r-rel0200a a074754 — changing test/mcp.test.ts's CommitLore-Version: 0.1.0 fixture trailer | that's protocol-version content inside a synthetic seed commit (what an old commit's trailer looked like), unrelated to and never asserted against package.json's version
• r-instci99a 318b9a2 — pre-installing curl/jq/tar/git in the containers before running install.sh | would hide exactly the gap this work exists to find — Debian ships neither curl nor wget by default, and asserting that failure cleanly is the point of the bare debian:stable-slim step, not an obstacle to route around
• r-instci99a 318b9a2 — publishing a -musl release target so Alpine could install successfully | a release.yml/build-matrix change, not an install.sh or CI-verification fix; out of scope here (DO NOT: no Docker in the release build matrix) and orthogonal to making the existing failure clear instead of a raw crash
• r-instci99a 318b9a2 — heuristically detecting musl before download (checking for /lib/ld-musl-*.so.1) | executing the freshly extracted, already checksum-verified binary directly is a stronger, more general check — it catches any reason the binary cannot run on this machine, not only the one musl signature this repository happens to know the path for
• r-instci99a 318b9a2 — a matrix job splitting debian/alpine | the two images need different assertions (debian: bare failure, then success once curl is added; alpine: one clean failure, nothing more to add) and share one staged release + HTTP server; one job with named, ordered steps keeps that shared setup and reads linearly in the log
• r-fix92dupid 7f41a6e — flagging every duplicate sha in a group regardless of payload, matching parse's labelRecordBlocks exactly | validate's own collision-check array pairs repositoryRecords (already carrying the message's last block once) with a per-block candidate; an unconditional duplicate-sha rule would flag the message's own single last block against its own re-derived copy, a false positive fixed instead by building ownRecords once per message rather than loosening the predicate past correctness
• r-fix92dupid 7f41a6e — reverting core/query.ts's collectRows dedup key back to sha+source+seq once findIdCollisions was fixed | that key was already wrong on its own terms (it does not match the trailers table's unique index), and leaving it in place would keep silently dropping a commit's second record block from any scoped-path context query, collision or not
• r-fix90shape 7f5766d — keeping the parent-count signal and also computing it for --message-file via .git/MERGE_HEAD | that only exists while a merge is in progress (the commit-msg hook's own scenario), not when re-validating an already-made merge commit's extracted message -- which is the issue's own reproduction and stays unreconciled under that approach
• r-fix93pkg 9c4a396 — repointing bin at dist/commitlore.mjs instead of removing it | that entry exists only to serve a package-manager install ADR-0011 already replaced with a git clone; repointing it keeps maintaining a path to an install mode that will never happen
• r-fix93pkg 9c4a396 — also removing files now | the issue's own "After B-09 · Single static binary — remove the Node runtime dependency #39" note groups bin/files/dependencies as one cleanup once the static binary lands; files alone is inert without a registry rather than actively broken, so doing it now means doing it twice
• r-distrace88 d118a73 — consolidating the four files' redundant tsc rebuilds into one vitest globalSetup | would remove the race for every file at once and is the more complete root-cause fix, but touches five files' bootstrap plus global config, and mcp.test.ts's beforeAll already tolerates unrelated in-flight tsc errors elsewhere in src/ (OWNED_SOURCES filtering) in a way a single shared build step cannot preserve without its own redesign — bigger blast radius than this issue asked for.
• r-distrace88 d118a73 — raising bench-ablation's timeout, globally or per-test | proven not to be a timeout problem at all: execFileSync blocks synchronously, so vitest's timeout mechanism cannot even engage against it (verified with a probe test); the actual failure is the runner subprocess legitimately exiting 1.
• r-parsemulti 6d39d25 — expanding findIdCollisions/index-db to flag a same-message duplicate id generally | reaches into query.ts's lifecycle fold and every consumer route (context, guard, stale) for a case bug-issue-89 only asked parse to surface; the smaller, requested fix is in parse alone.
• r-multirec01 92aeb24 — minting a fresh Record-Id for an inherited record that never declared one | no other code path in this project invents identity; Record-Id is always author-declared, and doing it here would be new scope beyond what the issue asked for
• r-multirec01 92aeb24 — a CI step comparing a PR's commits against its post-merge squash commit, as the primary mechanism for finding 1 | needs a GitHub API dependency this tool takes nowhere else, and can only run after the squash is already pushed; doctor catches the same mistake locally, before push, when the source branch is still in refs/heads
• r-plugman51 db8e2a1 — PreToolUse hook fires twice per edit | Claude Code's plugin loader dedups a manifest.hooks path that resolves (via realpath) to the already-loaded hooks/hooks.json before merging it, so the hooks array is never doubled; the redeclaration instead surfaced as a hook-load-failed PluginError under the loader's default strict mode
• r-exit065 e545dee — leaving guard's inversion in place and only documenting it | guard and inject are the two commands wired into hooks and CI, so a script written against guard today is already trusting the number; a documented inversion is still an inversion, and it gets load-bearing the longer it sits. The surface is one boolean per command right now — cheaper to fix once than to explain forever.
• r-m4n560 081d858 — n = 14 per arm | detecting only a two-thirds reduction is not a practically meaningful minimum effect
• r-6a29d5 31b1524 — keeping the leaking briefs and noting the caveat in the verdict | a null from a saturated design is uninterpretable — the effect could be absent, or both arms could have been told the answer
• r-4f71c8 74f7f39 — re-running M1's matrix with more seeds | 98 per arm at the observed base rate is 294 runs to answer a question a better instrument answers in 72
• r-4f71c8 74f7f39 — selecting the three tasks that did produce variance and reporting them | that is the post-hoc subset §4 forbids, and it is the specific dishonesty this file exists to prevent
• r-2b58d4 4842356 — exempting datasets written before the fields existed | it is one line and it deletes the guarantee
• r-8e15c2 70f6bcf — hashing only the files the entry point transitively imports | it is the same judgement call that produced this bug, made with more machinery
• r-9f52d7 2cd02e7 — reporting M3 with a caveat | a treatment that changed mid-run is a confound, not a limitation, and §4 forbids salvaging a result by narrowing the question after the fact
• r-9f52d7 2cd02e7 — stratifying rows by the dist they ran against | it would compare two arms across two products with n≈50 and no registered hypothesis for either half
• r-4a17d9 68d4c92 — guard versus the control as the primary test | it would confound the route with whether records exist at all, and the interesting question is which route works better once they do
• r-4a17d9 68d4c92 — a blocking guard arm | GUARD-CANNOT-BLOCK measured true and false positives in one score band; the only precision-safe threshold catches one in five
• r-8e04c1 5640748 — re-running M1-b's design at a larger n | it would buy precision on a delivery path the product does not use, which is the same mistake ROUTE-GAP identified and a bigger version of it
• r-4c73a2 1d82a5b — re-scoring the recorded transcripts and reporting the result | the labels would be chosen with the outcome known, which §4 forbids; the recorded runs were used only to check the surface behaves as intended
• r-4c73a2 1d82a5b — moving violation_if to code as well | it is instrumented-only, and changing an unregistered metric alongside a registered one makes it unclear which change any difference belongs to
• r-0d4b81 8005227 — a longer quickstart that demonstrates context, limits, ruled-out, warnings and stale | an agent calls those itself once the MCP server is registered, so listing them teaches the human a workflow that is not theirs
• r-3e8a41 2f0a8a0 — off-path records that advocate the ruled-out option | with no scoping they reach all three arms, raising re-proposal everywhere and compressing the grading and lifecycle contrasts the set is built to isolate
• r-2f8b90 a376808 — accept the inherited environment and document it | a memory server between runs is a confound, not a caveat
• r-2f8b90 a376808 — fail hard when the isolation flags are missing | an older CLI should still produce a run, as long as the log says it was not controlled
• r-9c2f74 d653153 — resume the pilot into the same file | a new process would load the edited code and create the mixing that had not happened
• r-9c2f74 d653153 — run the ablation arms as they stand | three nulls from comparing identical inputs read as "these guarantees do not matter"
• r-9c2f74 d653153 — keep the tasks that showed an effect and rewrite only the rest | the property is the criterion, not the direction of the result
• r-3f7a29 49817dc — repair a draft that fails verification | backfill's source material is weak enough that a repair loop would mostly be inventing
• r-3f7a29 49817dc — write reconstructed records into commit messages | history rewriting is irreversible and reaches every existing clone
• r-3f7a29 49817dc — post a fresh comment per push | it turns the signal into noise and the check gets muted
• r-5c8b31 60ddc39 — keep turns and explain it in prose | the JSONL outlives the prose, and whoever reads the rows later will not have it
• r-5c8b31 60ddc39 — drop the turn budget since it cannot be enforced | the overrun is still the signal that a run went off the rails
• r-6c2b95 5da793c — skip the dry-run driver | then nothing exercises the harness until a key exists, and the first real run debugs the harness instead of measuring anything
• r-6c2b95 5da793c — emit dry-run rows without a marker | indistinguishable from measurements the moment they leave the terminal
• r-c0f4e2 3d249cd — GitLore published as git-lore | the binary and search results still collide with the existing gitlore tool
• r-c0f4e2 3d249cd — keep Annals | the sound problem does not decay, and with code near zero this is the cheapest moment the project will ever have
• r-c0f4e2 3d249cd — rename code and spec first, documents later | the drift window makes every artifact written in it wrong
• r-b2e7f1 00d348d — line-matching Key: prefixes | prose containing a colon line parses as a record and feeds agents false context (verified B3)
• r-b2e7f1 00d348d — content-hash Record-Id | must survive rebase and squash, which a hash of the commit does not

Warnings (44)

• r-retireserena c1171ef (claim) — bench/results/ and the historical prose in bench/README.md and bench/PREREGISTRATION.md name .serena on purpose -- that is what the recorded runs saw; do not clean those mentions up
• r-rel071 af8e0ab (claim) — any option declared with a non-nullish default has the same shape, and nothing checks for it -- this fix repairs one site, not the class
• r-rel070 d4a4d8b (claim) — between the promotion merge and the tag push, every README install one-liner points at a tag that does not exist -- tag promptly and confirm the URL rather than assuming
• r-numgate b770054 (claim) — the gate matches p =, a pp figure and Fisher exact, so a future statistic in another shape -- an odds ratio, a chi-square -- would pass it and reintroduce the drift
• r-readmem5 6d04c0b (claim) — the sentence this replaces was the honest one for four releases, and its replacement will need the same treatment the day a task set nobody designed for discrimination gives a different answer
• r-clog070 172fa3d (claim) — the fixed list cites issue numbers rather than restating each defect, so a reader without network access gets a list of numbers
• r-4e7c19 6d4e828 (claim) — this closes the attribution half of blocker B only. W4 is still unmeasured, W3 is still unrecoverable for this corpus, and no figure in TOKEN-LEDGER.md section 9 changes
• r-4e7c19 6d4e828 (claim) — section 5 of TOKEN-LEDGER.md is pre-registration and was appended to, not edited — the floor has to stay visibly declared in advance
• r-nobin284 ab2f08f (claim) — an extensionless COMMITLORE_BIN is now ignored rather than honoured -- the hook falls through to the recorded install and to PATH, so a caller who pointed it at the wrapper still gets a working hook, by a different route
• r-hookfailopen 16963dd (claim) — this branch is what keeps a hook failure from blocking an edit -- if it ever needs to change, the replacement must still exit 0 and write nothing to stdout
• r-recov140 da5a210 (claim) — freeze independent gold before encoding any CommitLore record or the episode is invalid
• r-release030 510d70e (claim) — Tagging and publishing remain separate release steps.
• r-f61a2c 9114cf0 (claim) — keyword-strength is IDF-weighted keyword mass multiplied by unweighted distinctive-token coverage; do not restore the old identity label
• r-exposure52 ba69411 (claim) — guard exposure is instrumented in the benchmark hook adapter, not by changing guard scoring | M4 rows remain unexposed and metrics refuses their effect estimate
• r-rel0200a a074754 (claim) — scripts/commitlore-bootstrap.sh is orphaned -- no hooks.json entry invokes it, and its npm-install strategy contradicts ADR-0011. It still carries a live version default, now bumped for consistency, but nothing exercises it. Worth a follow-up issue: either wire it up correctly or delete it.
• r-instci99a 318b9a2 (claim) — the new binary-execution guard's die() message names musl/glibc specifically because that is the only way this repository's own release actually fails to execute today (glibc-only "-gnu" targets, verified against Alpine). If a -musl target is ever published, or the binary can fail to execute for an unrelated reason, this message will misdiagnose it — revisit the wording if that guard ever needs to distinguish causes.
• r-fix90shape 7f5766d (claim) — a message whose first line happens to start with one of these templates on a non-merge, non-CommitLore commit would also be excused if its trailer-shaped final paragraph were entirely unknown-key -- the same shape of risk bug-issue-76's original parent-count gate carried for genuine merge commits, now traded for one that is at least computable the same way everywhere
• r-distrace88 d118a73 (claim) — COMMITLORE_BENCH_DIST_DIR is read once at module load (bench/hooks-settings.ts DIST_DIR is a top-level const) — set it before importing the module, not after.
• r-parsemulti 6d39d25 (claim) — context and validate still do not catch two commit-sourced blocks in the current message sharing one Record-Id unless a notes mirror also disagrees (findIdCollisions requires a notes-sourced record in the group) — parse's check is intentionally independent, not a call into that function, so fixing this in context/validate is separate work.
• r-multirec01 92aeb24 (claim) — index-db.ts SCHEMA_VERSION is now 2 for the added block column — bump it again, not the shape in place, the next time the trailers table changes.
• r-plugman51 db8e2a1 (claim) — manifest.hooks/manifest.mcpServers in plugin.json exist only for files beyond hooks/hooks.json and .mcp.json; pointing either at its own conventional path reintroduces a hook-load-failed PluginError (hooks) or a no-op re-merge (mcpServers) — test/manifest.test.ts guards both
• r-exit065 e545dee (claim) — guard's swap is a breaking change for anything scripted against the old exit 2 for "matched" — see CHANGELOG Unreleased/Breaking
• r-m4n560 081d858 (claim) — 46/60 is the aggregate over all ten candidates; the eight qualifying tasks total 43/48
• r-6a29d5 31b1524 (claim) — briefs get shorter and harder to write, and work will be redone that a leaking brief would have got right the first time. That redo cost is the measurement, which is uncomfortable and correct
• r-4f71c8 74f7f39 (claim) — the prediction that real rejections raise the base rate may be wrong. If fewer than six tasks qualify, M4 does not proceed — a matrix of two tasks is a result about two tasks
• r-4f71c8 74f7f39 (claim) — a positive result licenses one sentence, that records delivered before an edit reduce revival of a rejected approach. It does not license "makes agents better" or any figure about time saved. This project withdrew one set of numbers for running ahead of its evidence
• r-2b58d4 4842356 (claim) — this leaves the README with no measured numbers at all until M3-b runs. That is the honest state and it is also a worse first impression. The alternative was publishing numbers produced by a binary nobody recorded
• r-8e15c2 70f6bcf (claim) — this is the second time in two commits that a fix for the M3 failure did not actually cover the M3 failure. The first was caught by testing the fix against the incident rather than against its own tests
• r-9f52d7 2cd02e7 (claim) — this is the fourth defect this week of one shape — the thing being verified and the thing actually in play had drifted apart. A check that read a decision's inputs; a doctor that probed the developer's artifact instead of the user's; a scanner keyed to one field of a record whose every field was a surface; and now a benchmark reading a binary its own operator was rebuilding
• r-4a17d9 68d4c92 (claim) — both hooked arms pay a subprocess per edit. M2 put all three of its timeouts in its hooked arm, and a timeout truncates a run, which flatters whichever arm suffers it — stated before the numbers exist
• r-8e04c1 5640748 (claim) — M2's numbers do not continue M1-b's — different delivery path, so they are three measurements and not a series
• r-4c73a2 1d82a5b (claim) — SURFACES in task-loader.ts and MatchSurface in types.ts are two lists of the same thing — adding a surface means editing both
• r-0d4b81 8005227 (claim) — claude mcp add commitlore -- commitlore mcp is Claude Code's syntax — other MCP clients register a stdio server their own way
• r-8b41e6 0bbad66 (claim) — the payload share and the fixture share are not interchangeable — the payload adds framing and drops what grading and lifecycle withhold, so a reader who swaps one for the other will be wrong by a small, plausible margin
• r-5c07d2 9ec184a (claim) — the off-path share here is measured over trailer-block characters in the fixtures, not over the assembled payload — the two differ by framing and by what grading and lifecycle withhold, so do not quote one for the other
• r-3e8a41 2f0a8a0 (claim) — the ablation set is a different synthetic repository from bench/tasks, so its commitlore-on arm must never be pooled with the primary matrix's
• r-2f8b90 a376808 (claim) — if the runner log carries the "does not support" warning, the rows are not environment-controlled -- do not compare them to rows that are
• r-9c2f74 d653153 (claim) — after the measurement, check that git status is clean and the recorded sha is still HEAD -- an edit mid-run breaks reproducibility silently, and that check is the only thing that catches it
• r-3f7a29 49817dc (claim) — every backfilled record is Provenance: reconstructed, which the trust model always renders as a claim -- do not add a path that lets a draft override that field
• r-5c8b31 60ddc39 (claim) — a driver that gains a real turn limit should stop emitting over-turns and start emitting an enforced label -- do not reuse over-turns for something the harness actually stopped
• r-6c2b95 5da793c (claim) — never cite a row with simulated:true -- README numbers come from bench/results logs and those rows are not results
• r-c0f4e2 3d249cd (claim) — ADR-0008 and ADR-0009 keep the literal string Annals on purpose -- mechanical substitution there destroys the decision trail
• r-c0f4e2 3d249cd (claim) — the residual grep for lore_query reports a false positive because commitlore_query contains it as a substring, so check the prefix
• r-b2e7f1 00d348d (claim) — spec/fixtures and spec/contract-cases are the contract -- prose in SPEC.md explains them, it does not define them

git log --follow accepts exactly one pathspec, so renames are not followed for 7 paths; query one path at a time to follow its rename chain

_{Trailer violations fail this check. Active constraints are informational — they are what the repository already decided, not a verdict on this PR.}