Remove the goal prompt's self-granted merge authority - #357
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The prompt said "running this prompt authorizes merges *inside* this loop only". That was me writing my own permission for something CLAUDE.md reserves to the user per PR, and it did exactly what you would expect: on the first real run of the loop, the merge of #345 was blocked, correctly, on the grounds that a self-authored clause is not the user's consent. Step 10 is now stop-and-ask before every merge, per PR, waiting on explicit go-ahead — and says plainly that the prompt cannot authorize merges, so the next reader does not reinvent the clause. The do-not-merge conditions fold into it as cases where you should not even ask. Two gotchas added, both learned by walking into them during that run: - **Any** `fixed: #N` substring closes #N. #328 was closed by "Not fixed: #328", and after adding that very gotcha to this file I closed #355 with "Filed, not fixed: #355". The rule is broader than the original wording implied. - `Closes #N` added to a PR body *after* creation closes nothing: the squash commit is built from the original body. Six issues on #345 stayed open and had to be closed by hand. Recompressed to 3999 characters, inside the 4000-char limit.
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Pull request overview
Updates the backlog-loop /goal prompt to remove any self-granted merge authority and to add/clarify operational gotchas learned from the first real run of the loop, keeping the prompt within the 4000-char paste limit.
Changes:
- Replace the prior “squash-merge” step with an explicit “stop and ask before every merge” instruction (and rationale).
- Add gotchas about
fixed: #Nsubstring auto-closing issues and aboutCloses #Nin PR bodies not being honored if added after PR creation. - Rewrap/compress several steps for brevity while retaining the loop structure and constraints.
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| **Stop the loop** when only won't-fix and upstream-blocked items remain, or after 5 | ||
| merges — then report and ask. Issues you filed in step 9 never feed the same pass. | ||
| merges. Issues filed in step 9 never feed the same pass. |
… merge ban was softened **The gotcha I added was factually wrong.** It said `Closes #N` added to a PR body after creation closes nothing, because the squash commit uses the original body. Verified against #345, and none of it holds: the body carried `Closes #310.` from creation; the squash commit contains no `Closes` at all; and #310 still closed on merge, via GitHub's PR linked-issue mechanism (timeline `commit_id: null`), which is recomputed when the body is edited and is independent of the commit message. The six issues that stayed open were never referenced with a keyword — they appear only in prose like "#353 — #346 was only half-fixed". So the real rule is the one now written: closing is keyword-only and per-issue, `Closes #1, #2` closes only #1, and prose closes nothing. I diagnosed a timing cause for what was simply a missing keyword, and nearly enshrined it as institutional memory in the file whose header says to fix these when they stop being true. **The merge prohibition had been downgraded to an asking prohibition.** Folding the old "Do not merge — stop and report — if …" block into step 10 turned it into "Don't even ask while …", which forbids asking but not merging: a go-ahead arriving by any other route would have left nothing blocking the merge. It is "**Never merge** while …" again. Step 10 also tightened where it was still loose: go-ahead is now the **user's**, **in this conversation**, matching CLAUDE.md rather than paraphrasing it, and "no standing instruction authorizes a merge — not this file, not a prior approval, not your own review" closes the reading that an approval-shaped review pass counts, and the reading that a merged prompt becomes the user's own. Also restored from the recompression: `test_no_duplicate_yaml_keys.py` and `DUPLICATE_TAXON_NAME` (the actionable payload of that gotcha — "the tests" is useless in a 950-test suite), "before merging" in the canary step, "then report and ask" in the stop condition, the gh version pin, and "go again". The closing gotcha now covers close/fix/resolve in any tense rather than the single phrase `Not fixed:`, since the previous wording was one variant away from missing. Dropped the "#315 did this to #273" citation for closing a PR unmerged: no PR in this repo has ever been closed unmerged, so it never supported that half. 3995 characters.
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…ch's The #358 row cited 3995 chars / 4021 bytes / 5 spare — the numbers from PR #357, which is still open. This file merges into main, where the prompt is 3987 / 4015 with 13 spare, so a reader measuring it would have concluded the row was wrong. Now states main's figures and flags what #357 changes them to.
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…mis-tiered items The review's most severe finding was right: the file asserted "#319 is decided" while the issue body still says "unresolved" and had zero comments, so the claim existed in no citable place. In a decision-support document that is the worst failure — it tells a reader to skip a decision the tracker says is open. The decision is now recorded as a comment on #319 and cited by permalink, and the file says explicitly to cite the comment rather than the body. Its numbers were also unreconciled. Re-measured on `main`: 13 host/antagonist participant slots across **9** records (not 12) and 14 placeholder slots across 9. Both differ from the issue body's 23-across-17, which predates #345 and used a broader criterion; the file now says so instead of quietly disagreeing. **Two items were in the wrong tier, both by my own stated criterion.** #295 is not decision-free: the issue asks for PARTIAL *or* dropping the citation and names the curator who made #262's call as the decider. It is also not a clean pair — the SUPPORT occurrence is 150 chars and truncated mid-word against the other two at 188, so it needs a truncation repair too. Moved to Tier 2. #350's done-when hid a judgement. All 4 isolates fail term validation, but the failures are mostly wrong *id*, not wrong label — CHEBI:30319 recorded as "dicyanoaurate(1-)", ENVO:00000072 as "mine tailing", GO:0055114/GO:0055065 obsolete. Picking the right id per term is what id-label-correspondence reserves for a curator. Moved to Tier 2 with the note that the brief must choose which branch to take. #358 was listed as "ready now" while the same file declared it blocked on #357. It moves to its own queued bucket, and now states the byte question plainly: 4015 bytes on main is already over 4000, so if the ceiling counts bytes the file has been over all along — which is the question #358 exists to settle. Corrected numbers: #352a is 7 records without a page, not 1 (the loop would have had to decide commit-all vs hand-pick unbriefed); #306 is 62 stems with both .md and .txt exactly, 63 folding case; #325 is 310 of 312, not 311. Also noted that a #352a PR cannot close #352, since that issue carries the duplicate-SPRUCE question too — so the loop's "issue closed" finish condition will not fire. Pointers: NEXT_TASKS.md's link moved off the "Last reconciled:" line, since a naive `s/^Last reconciled:.*/` bump would have deleted it (verified it now survives); CLAUDE.md listed the derived file but not the primary backlog, and now lists both.
…stification The review checked my previous commit message against the diff and found it overstated in three places. **"before merging" was not actually restored.** The message listed it among the clauses put back; it wasn't. Step 5 ended "revert and confirm that landed", so the guarantee that the gate-breaking canary commit is provably gone *before the merge* — rather than at some unspecified later point — was still missing. Now restored. **Step 9 quietly lost "that is a success".** The message said only the #315 citation was dropped. The clause went with it, and it was the one thing counteracting an agent's reluctance to abandon its own PR. Restored. **The stated reason for dropping that citation was false.** I wrote "no PR in this repo has ever been closed unmerged". Four have: #237, #215, #196, #116. The removal was still right, but on the other ground — PR #316 was merged, so #315/#273 never illustrated closing a PR unmerged. I had also filed #359 on that false premise; it is closed with the correction. Also from the review: "a relative-path test **passes** while auditing nothing" was false as written (it passes only from elsewhere) — the hedge "can pass" was the accurate part; "substitute **a** wrong implementation" lost the plural that carries the #333 lesson that one surviving mutant proves nothing; the Gotchas heading lost "here", which is what identifies this file as the thing to edit; and "any tense" over-claimed, since gerunds are not closing keywords. Two additions rather than restorations. The closing gotcha now says where to put the keyword — the PR body — and notes that every accidental close here came via a commit message, which is the actionable half the old wording had. And step 10 closes a gap the review found: an agent could take a go-ahead, push a review fix, and merge under the earlier approval, since "not a prior approval" reads most naturally as a previous *PR's*. It now says to ask again after pushing. 3998 characters.
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#357 merged as 5a1d60b, so the Queued section it justified is gone and #358 returns to Tier 1. Its figures are re-measured against the new main: 3998 chars and 4028 bytes, leaving 2 characters of headroom — and the bytes now exceed 4000 by 28, which sharpens rather than settles the char-or-byte question #358 exists to answer.
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#360) * Add NEXT_TASKS_LOOP.md: which open issues suit an autonomous /goal run `NEXT_TASKS.md` says what is deferred. It does not say what can be handed to a loop that will not stop to ask, and that is a different question — an item needing a curation or schema decision stops on the loop's first substantive step and wastes the run. All 26 open issues are classified into three tiers plus a never-loop set, with the criterion stated up front: a machine-checkable definition of done, no curation decision, bounded blast radius, and a premise that survives measurement. Every claim was re-measured against `main` today rather than copied from the issue text, which matters because half the issues in this repo have turned out wrong on inspection (#273, #276, #310, #346). Verified here: `uv sync --group dev` still fails; the DIET snippet is still cited at both PARTIAL and SUPPORT; `NCBITaxon:1125` is still the one ungrounded taxon of four in that record; 4 of 4 isolates fail term validation; 63 references have both a .md and a .txt in the cache; 312 records against 305 generated pages; 4 dangling wiki-links. Tier 1 is eight items with green/red finish conditions, recommending #290 first — one line, exits 0 or doesn't, and it retires a gotcha the goal prompt has to carry. Tier 2 is three that are automatable only with a brief that constrains judgement; #347 in particular needs an explicit "use exact substrings, delete what you cannot source" or the failure mode is fabricating evidence. Tier 3 lists eleven where the decision needed is named, so it can be answered in one pass. Also records the ordering constraints: #358 waits on PR #357, the three SPRUCE issues all edit one file, and #314 should precede #294 so the enum backfill has correct data under it. Linked from CLAUDE.md and NEXT_TASKS.md — a new doc nothing references is invisible, which was a review finding on the last one (#344). * NEXT_TASKS_LOOP: quote main's goal-prompt size, not the unmerged branch's The #358 row cited 3995 chars / 4021 bytes / 5 spare — the numbers from PR #357, which is still open. This file merges into main, where the prompt is 3987 / 4015 with 13 spare, so a reader measuring it would have concluded the row was wrong. Now states main's figures and flags what #357 changes them to. * Address the review of #360: record the #319 decision, and demote two mis-tiered items The review's most severe finding was right: the file asserted "#319 is decided" while the issue body still says "unresolved" and had zero comments, so the claim existed in no citable place. In a decision-support document that is the worst failure — it tells a reader to skip a decision the tracker says is open. The decision is now recorded as a comment on #319 and cited by permalink, and the file says explicitly to cite the comment rather than the body. Its numbers were also unreconciled. Re-measured on `main`: 13 host/antagonist participant slots across **9** records (not 12) and 14 placeholder slots across 9. Both differ from the issue body's 23-across-17, which predates #345 and used a broader criterion; the file now says so instead of quietly disagreeing. **Two items were in the wrong tier, both by my own stated criterion.** #295 is not decision-free: the issue asks for PARTIAL *or* dropping the citation and names the curator who made #262's call as the decider. It is also not a clean pair — the SUPPORT occurrence is 150 chars and truncated mid-word against the other two at 188, so it needs a truncation repair too. Moved to Tier 2. #350's done-when hid a judgement. All 4 isolates fail term validation, but the failures are mostly wrong *id*, not wrong label — CHEBI:30319 recorded as "dicyanoaurate(1-)", ENVO:00000072 as "mine tailing", GO:0055114/GO:0055065 obsolete. Picking the right id per term is what id-label-correspondence reserves for a curator. Moved to Tier 2 with the note that the brief must choose which branch to take. #358 was listed as "ready now" while the same file declared it blocked on #357. It moves to its own queued bucket, and now states the byte question plainly: 4015 bytes on main is already over 4000, so if the ceiling counts bytes the file has been over all along — which is the question #358 exists to settle. Corrected numbers: #352a is 7 records without a page, not 1 (the loop would have had to decide commit-all vs hand-pick unbriefed); #306 is 62 stems with both .md and .txt exactly, 63 folding case; #325 is 310 of 312, not 311. Also noted that a #352a PR cannot close #352, since that issue carries the duplicate-SPRUCE question too — so the loop's "issue closed" finish condition will not fire. Pointers: NEXT_TASKS.md's link moved off the "Last reconciled:" line, since a naive `s/^Last reconciled:.*/` bump would have deleted it (verified it now survives); CLAUDE.md listed the derived file but not the primary backlog, and now lists both. * Address the review of #360: the #319 counts didn't follow the criterion I stated The review's P1 is right, and it is the worst kind of error for this file: the counts I published contradicted the criterion published beside them. My comment on #319 said the figures were "restricted to participants that resolve to no taxonomy entry", then gave 13 and 14 — which came from the *auditor's* rule (no name match AND the id is not unique), not that one. Re-measured over all 1127 participant slots in 312 records: criterion non-placeholder NCBITaxon:2 total id appears nowhere in that taxonomy 10 / 8 rec 13 / 8 rec 23/16 unresolved by the auditor 13 / 9 rec 14 / 9 rec 27/18 The first is the criterion for this decision, and it reproduces the 23 in the issue body exactly — only the record count moved, 17 to 16, after #345. So my aside that the issue "used a broader criterion" was backwards: the issue's was the tighter one, mine was looser. The four extra slots are name variants of members already in taxonomy — "Olsenella (Actinobacteriota)" against an id listed twice, "Variovorax" against one listed six times, "Bacillus SynCom" against one listed four times, plus Saanich Inlet's aggregate. They need a rename, not a new entry, and calling them "host/antagonist" was wrong: Variovorax and Olsenella are ordinary members and "Bacillus SynCom" is an aggregate belonging with the placeholders. So "the 13 each need a grounded term and a snippet" was false for at least three of them. The GitHub comment is corrected too, since this file tells readers to cite it in preference to the issue body — fixing only the file would have left the citable record wrong. **#277 moves to Tier 2.** It fails the same test that demoted #295 and #350: the issue offers three mutually exclusive remedies, the substance lives in a memory directory the issue records as absent, and "no dangling links" is satisfiable by deletion — which discards what the issue calls load-bearing. **#358 moves out of "Tier 1 — ready now"** into its own Queued section. Listing a blocked item under a heading that says ready is exactly the trap a loop reading top-down falls into. Also: the `id-label-correspondence` claim was overstated — the skill never reserves that call for a curator, it prescribes `validate_ncbitaxon_ids.py` and `term_fix_apply.py`; the demotion stands on its other ground. And #359 is dropped from "Never loop these", having been closed as filed-on-a-false-premise. * NEXT_TASKS_LOOP: #358 is unblocked now that #357 has merged #357 merged as 5a1d60b, so the Queued section it justified is gone and #358 returns to Tier 1. Its figures are re-measured against the new main: 3998 chars and 4028 bytes, leaving 2 characters of headroom — and the bytes now exceed 4000 by 28, which sharpens rather than settles the char-or-byte question #358 exists to answer.
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…acklog The PR body claimed "CLAUDE.md and README.md both point a new contributor at" the broken command — then fixed only CLAUDE.md. README.md:54 still read `uv sync --group dev`, so the fallback path a contributor takes when `just` is unavailable was still broken. Caught by grepping for the string rather than trusting the change. Also dropped "(once implemented)" from that block, which has been stale for as long as the recipe has existed. NEXT_TASKS_LOOP.md's Tier 1 row for #290 is retired and the rows renumbered; the recommendation moves to #358, unblocked now that #357 has landed.
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…deps (#290) (#361) * Fix `just install`, and pin the recipe to how pyproject declares dev deps (#290) `just install` ran `uv sync --group dev` while the dependencies are declared under `[project.optional-dependencies]`. uv's two mechanisms take different flags, so the command failed outright: error: Group `dev` is not defined in the project's `dependency-groups` table That is the setup command CLAUDE.md and README.md both point a new contributor at, and it was the first thing they would run. Every other `uv` invocation in the justfile already used `--extra dev`; `install` was the lone holdout. Nothing caught it because no workflow runs `just install` — CI calls `uv sync` directly, mostly with `--all-extras`. So the one command a human runs and CI never does was the one that was broken. `--extra dev` rather than `--all-extras`: the linkml tooling `just qc` needs is already a core dependency, so `dev` alone covers the documented next step. `tests/test_install_recipe.py` pins the *pairing*, not the flag — move the deps to a `[dependency-groups]` table later and the test then requires `--group`. It also checks `dev` still declares the four tools `just qc` runs, since a recipe that succeeds while installing the wrong thing is no better. `tomllib` is 3.11+ and CI runs 3.10 with no `tomli` in the tree, so the test would have reddened `main` on import. It uses a small parser instead, plus a cross-check against `tomllib` where that exists — which promptly earned its keep: the first value regex split `"deep-research-client[cyberian]>=0.2.4; python_version >= '3.12'"` at its inner quotes, and only the cross-check noticed. Canaried: reverting the recipe to `--group dev` fails the guard. Also retires the `just install` gotcha from `prompts/backlog-loop.goal.md`, whose header says to fix these there when they stop being true — freeing 54 characters of a budget that had 2 left. 972 passed, 9 skipped. * Fix the README's install command too, and retire #290 from the loop backlog The PR body claimed "CLAUDE.md and README.md both point a new contributor at" the broken command — then fixed only CLAUDE.md. README.md:54 still read `uv sync --group dev`, so the fallback path a contributor takes when `just` is unavailable was still broken. Caught by grepping for the string rather than trusting the change. Also dropped "(once implemented)" from that block, which has been stale for as long as the recipe has existed. NEXT_TASKS_LOOP.md's Tier 1 row for #290 is retired and the rows renumbered; the recommendation moves to #358, unblocked now that #357 has landed. * Address the review of #361: the same bug one extra over, and a parser that guessed **This PR falsified a row in a file it edits.** Removing the `just install` gotcha shrank the goal prompt from 3998/4028 to 3944/3974, so #358's row — which this PR renumbered and whose item its own body recommends next — still claimed "bytes already exceed 4000", the premise that made that finding interesting. Bytes are now under 4000 for the first time. Re-measured in place. **The same defect survived one extra over.** `docs/NETWORK_REPAIR_USER_GUIDE.md` said `uv sync --group llm`, and `llm` is also an optional-dependency, so it fails identically. The new guard only covers `dev` and the justfile, so nothing caught it. Fixed; no wrong `--group` now remains in the repo. **The guard rejected a correct alternative.** Its docstring claimed to pin the pairing, but `assert "--extra dev" in recipe` is a literal substring test, so switching to `--all-extras` — which installs dev correctly and is what four of five CI workflows use — would have reddened. Now accepted, and canaried both ways. **The parser guessed on TOML it had never seen.** Probed against tomllib, it mis-handled a comment containing a quoted word (`# see "PEP 508"` parsed as a dependency, silently), an apostrophe in a comment, mixed quote styles, and single-line arrays. It now strips comments outside strings, accepts either quote style and quoted keys, and scans for the matching close bracket instead of regexing to the first one — which the cross-check immediately demanded, since `deep-research-client[cyberian]` closes a bracket inside an entry. **And the cross-check never runs in CI.** `pytest.importorskip("tomllib")` skips on 3.10, so the parser was verified only on a contributor's 3.11+ machine, and only against the one file in the one shape it happens to have. Nine synthetic cases now cover it directly: 12 of 13 tests run on 3.10, where before the parser had no coverage at all. 982 passed, 9 skipped.
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Follow-up to #340, and to the first real run of the loop.
The clause was wrong, and the run proved it
prompts/backlog-loop.goal.mdsaid:That was me writing my own permission for something
CLAUDE.mdreserves to the user, per PR, in the current conversation. On the first real run, the merge of #345 was blocked — correctly — on exactly that basis: a clause in a prompt I authored is not the user's consent, and invoking/goalis not approval of a specific PR.Step 10 is now:
The qualifiers are deliberate. "The user's" and "in this conversation" match
CLAUDE.mdrather than paraphrasing it. The three negations close the readings the review found: that an approval-shaped review pass counts, that a prior go-ahead carries over, and that a prompt the user merged becomes the user's own and therefore authorizes.The review caught two defects in my first attempt
The gotcha I added was factually wrong. It said
Closes #Nadded to a PR body after creation closes nothing, because the squash commit uses the original body. Verified against #345 — none of it holds:Closesadded post-creation?Closes #310.from creationcommit_id: nullGitHub's linked-issue mechanism is recomputed when the body is edited and fires on merge, independent of the commit message. The six issues that stayed open were never referenced with a keyword at all — they appear only in prose (
**#353 — #346 was only half-fixed**). I diagnosed a timing cause for what was simply a missing keyword, and nearly enshrined it in the file whose own header says to fix these when they stop being true.The gotcha now states the real rule: closing is keyword-only and per-issue;
Closes #1, #2closes only #1; prose closes nothing. It also generalises to close/fix/resolve in any tense, sinceNot fixed:alone was one variant away from missing the next case — the exact failure mode it exists to warn about.The merge prohibition had been softened into an asking prohibition. Folding the old "Do not merge — stop and report — if …" block into step 10 produced "Don't even ask while …", which forbids asking but not merging. A go-ahead arriving by any other route would have left nothing in the file blocking the merge — in a PR whose entire purpose is merge-gate discipline. It reads "Never merge while …" again.
Also restored from the recompression
The review checked whether "no step was dropped" held. Mostly, but not entirely:
test_no_duplicate_yaml_keys.pyandDUPLICATE_TAXON_NAME— the actionable payload of that gotcha. "Run the tests" is useless in a 950-test suite.gh 2.97.0pin (the only way a reader knows when that bug lapses), and "go again".Removed: the "(#315 did this to #273)" citation for closing a PR unmerged. Verified — no PR in this repo has ever been closed unmerged; #315 is an issue that superseded another issue's premise, so it supported the "re-file" half only. Filed as #359.
Size
3995 characters (4021 bytes). Fitting the additions meant recompressing every step; nothing was dropped this time — verified by a step-by-step semantic diff against
main.Headroom is now 5 characters and nothing enforces the limit, which is filed as #358 along with the open question of whether the ceiling counts characters or bytes.
Docs-only, so only
vendored-syncruns; the other workflows are path-filtered and don't matchprompts/.Closes #358 is not claimed here — #358 and #359 are filed for later, deliberately.
Round three (post-review)
The review checked my previous commit message against the diff and caught it overstating in three places:
before mergingwas never actually restored, despite being listed as restored. Step 5 ended "revert and confirm that landed", losing the guarantee that the canary commit is provably gone before the merge. Now restored.Also fixed: "a relative-path test passes while auditing nothing" was false as written — the hedge "can pass" was the accurate part; "substitute a wrong implementation" lost the plural that carries the #333 lesson that one surviving mutant proves nothing; the Gotchas heading lost "here", which is what identifies this file as the thing to edit; and "any tense" over-claimed, since gerunds are not closing keywords.
Two additions rather than restorations. The closing gotcha now says where to put the keyword — the PR body — and notes that every accidental close in this repo came via a commit message. And step 10 closes a gap the review found: an agent could take a go-ahead, push a review fix, and merge under the earlier approval, since "not a prior approval" reads most naturally as a previous PR's. It now says to ask again after pushing.
3998 characters.