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fix(skills): publish runtime skill dirs atomically so no reader sees a tree without SKILL.md (BLO-32167) - #1699

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fix(skills): publish runtime skill dirs atomically so no reader sees a tree without SKILL.md (BLO-32167)#1699
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@allyblockcast allyblockcast Bot commented Sep 7, 2026

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Thinking Path

  • Paperclip is the open source app people use to manage AI agents for work
  • Company skills are materialized to disk per company under __runtime__/<slug>/, then hashed into a prompt-bundle cache key and snapshotted into each agent pod
  • materializeRuntimeSkillFiles published that directory in placefs.rm(recursive)mkdir → per-file writeFile — so the rolling sweep left the published path observable in a half-written state
  • fix(claude-k8s): classify a mid-materialization skill fault instead of adapter_failed (BLO-32055) #1669 (BLO-32055) closed the instant of that window which throws ENOENT, but a reader sampling a moment earlier sees an existing directory with no SKILL.md and nothing throws at all, so no try/catch can reach it
  • The bundle key is minted over the unusable tree, cached under it, and the run proceeds silently degraded — BLO-7991's original harm, with no failure for anyone to see
  • This pull request makes the publish atomic at the writer and adds a positive-shape backstop at the reader
  • The benefit is that the state stops existing rather than being detected after the fact, and where it can still arrive from another code path it now classifies as the retryable fault it is

Linked Issues or Issue Description

Duplicate search

Searched Blockcast/paperclip open PRs for skill, materializ, prompt-cache, hashPath, 32167. The two hits are unrelated to this branch: #1684 (skill propagation docs) and #1679 (BLO-31993, the absent mislabel in the heartbeat notice). No open PR touches materializeRuntimeSkillFiles or the bundle-key walk.

What Changed

  • server/src/services/company-skills.tsmaterializeRuntimeSkillFiles writes into a dot-prefixed staging sibling and publishes via a new publishStagedRuntimeSkillDir, which renames the outgoing tree aside, renames the staging tree in, then removes the retired tree. Concurrent-publisher collisions (ENOTEMPTY/EEXIST) take the slot; any other rename failure rolls the outgoing tree back.
  • The !wroteSkillFile branch deliberately still removes the published tree, exactly as before — a skill whose stored SKILL.md has gone must stop being served, and resolveRuntimeSkillSource would otherwise keep resolving the stale directory.
  • vendor/paperclip-adapter-claude-k8s/src/server/prompt-cache.ts — new assertSkillEntrypointPresent: a catalog-backed skill source must carry a readable SKILL.md at its root, else ClaudeSkillSourceUnavailableError with catalogBacked: true (retryable skill_materialization_pending). Runs only for keys explicitly in catalogBackedSkillKeys.
  • Tests in both packages, each verified as a negative control (below).
  • PROVENANCE integrity hash updated, change-log row added, version bumped to 0.2.6-blockcast.4.

Two design choices worth reviewing

Rename-aside, not rm-then-rename. The RCA framing in #1669 pointed at materializePaperclipSkillCopy, which does fs.rm(targetRoot, {recursive:true}) then rename, under a writer lock. Ported literally that does not fix this issue: the lock serializes writers, and rm is itself a walk, so a concurrent reader mid-rm sees a shrinking tree — branch B survives the port. Renaming the outgoing tree aside is reader-atomic without needing writer exclusion, so no lock is used. The residual is one instant where the directory is absent, which every reader already handles as retryable.

The backstop keys on SKILL.md, not on emptiness. The writer iterates fileInventory in order and SKILL.md need not be first, so the far commoner partial state is some files, no entrypoint — an emptiness test walks straight past it. Asserting the positive shape is also the BLO-31794 inversion applied here.

Verification

# vendored adapter (CI: "Vendored claude_k8s adapter")
cd vendor/paperclip-adapter-claude-k8s && npm ci --include=dev
npx --no-install tsc --noEmit            # clean
npm test                                 # 14 files, 845 tests passed

# server (CI: "General tests (server)")
cd server && npx tsc --noEmit -p tsconfig.json   # clean
npx vitest run src/__tests__/company-skills-service.test.ts \
  src/__tests__/company-skills.test.ts src/__tests__/company-skills-routes.test.ts \
  src/__tests__/company-skills-catalog-service.test.ts \
  src/__tests__/company-skills-detail.test.ts     # 5 files, 128 tests passed

Negative controls. Each new test was re-run against the pre-fix source to prove it discriminates the change rather than passing alongside it.

test vs. pre-fix source
never publishes a runtime skill directory without SKILL.md FAILSexpected [ { exists: true, hasSkillFile: false } ] to deeply equal [], a direct capture of branch B
refuses to mint a key over a catalog-backed skill whose directory is empty FAILS — mints a key
refuses a partially-written tree that has files but no SKILL.md FAILS — mints a key
does not launder a non-ENOENT stat failure into a skill fault FAILS — wrong error type
leaves a non-catalog-backed empty directory classifying exactly as before passes both — no-regression guard
leaves the bundle key of a populated catalog-backed tree byte-identical passes both — no-regression guard
accepts a SKILL.md reached through a symlink passes both — no-regression guard
leaves no staging or retired trees behind in __runtime__ passes both — guards the new code only; there is nothing to leak pre-fix

The server-side test asserts what a concurrent reader can see rather than how the writer is implemented: it samples the published directory from inside fs.writeFile, before the write lands, during a re-materialization. It carries an explicit expect(samples.length).toBeGreaterThan(0) so it cannot pass vacuously if the writer stops calling writeFile or the second listing stops re-materializing.

Manual repro from the issue (stat the store and a pod copy during a sweep) is not reproducible on demand and was not run; the in-band substitute is the sampled window above.

Risks

  • Behaviour deliberately preserved, not improved: the !wroteSkillFile path still deletes the published tree. Staging would have let the previously-good tree survive a transient DB read failure, which is arguably better, but it is a semantic change unrelated to this issue and is not smuggled in here.
  • Scope limit — materializeVersionSnapshot is unchanged and still has the original non-atomic shape. It publishes to a content-addressed __versions__/<skillId>/<versionId>/ path with a fingerprint early-return, so it rewrites far more rarely, but the same race exists there. Left out to keep this diff reviewable; the adapter backstop covers the reader side of it.
  • Scope limit — packages/adapters/claude-local/src/server/prompt-cache.ts has its own copy of the walk and received neither fix(claude-k8s): classify a mid-materialization skill fault instead of adapter_failed (BLO-32055) #1669's guard nor this one. Consistent with fix(claude-k8s): classify a mid-materialization skill fault instead of adapter_failed (BLO-32055) #1669's scope; flagging rather than silently widening.
  • AC2 is closed by removal, not by a catalogue change. resolveExistingSkillDirectory already required SKILL.md, so the server listing was never the leak; the observed advertisement came from the pod's snapshot of an already-published tree. With atomic publish there is no incomplete tree to snapshot. No suppression logic was added, so nothing new can hide a skill.
  • New on-disk artifacts: dot-prefixed .staging-* / .retired-* siblings inside __runtime__. Dot-prefixed because a runtime name never starts with a dot, so they cannot be mistaken for a skill; nothing in the tree enumerates __runtime__ today, and a test asserts the root settles to exactly the published directory. A hard-killed process could leak one; they are uniquely named per pid+uuid so they cannot collide or be reused.
  • Low risk to the hot path: the backstop adds one stat per catalog-backed skill per bundle-key build, and a test pins the key byte-identical for a healthy tree — a changed key would invalidate every cached prompt bundle in the estate on deploy.

Model Used

Claude Opus 4.5 (claude-opus-5[1m], 1M context, extended thinking, tool use), running as the Paperclip CTO agent via the claude_k8s adapter.

Checklist

  • I have included a thinking path that traces from project context to this change
  • I have specified the model used (with version and capability details)
  • I have checked ROADMAP.md and confirmed this PR does not duplicate planned core work
  • I have searched GitHub for duplicate or related PRs and linked them above
  • I have either (a) linked existing issues with Fixes: # / Closes # / Refs # OR (b) described the issue in-PR following the relevant issue template
  • I have run tests locally and they pass
  • I have added or updated tests where applicable
  • If this change affects the UI, I have included before/after screenshots — n/a, no UI surface
  • I have updated relevant documentation to reflect my changes (PROVENANCE.md change-log row + integrity hash + version bump)
  • I have considered and documented any risks above
  • All Paperclip CI gates are green — pending first run
  • Greptile is 5/5 with no open P2s, recommendations, or follow-ups — pending review
  • I will address all Greptile and reviewer comments before requesting merge

@allyblockcast
allyblockcast Bot requested a review from kkroo as a code owner September 7, 2026 05:33
@allyblockcast

allyblockcast Bot commented Sep 7, 2026

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@ally please review at head 18822b5 — BLO-32167, the second branch of the skill-materialization race.

Three things I would most like challenged:

  1. The publish swap in publishStagedRuntimeSkillDir (server/src/services/company-skills.ts). I deliberately did not port materializePaperclipSkillCopy's rm-then-rename-under-lock pattern, because its lock serializes writers while rm is itself a walk — a concurrent reader mid-rm still sees a shrinking tree, which is exactly the defect this issue is about. Is the rename-aside sequence correct under concurrent publishers, and is the ENOTEMPTY/EEXIST retry plus the rollback-on-other-errors right? Is dropping the lock entirely defensible?

  2. The scope of the new assertSkillEntrypointPresent guard. It fires only when the key is explicitly in catalogBackedSkillKeys, never on the ?? true default the branch-A classifier uses — my reasoning is that the default is right for classifying a fault that already happened but wrong for manufacturing one, since erring toward manufacturing would fail runs over bundled adapter skills in a read-only image path (BLO-31794). Is that asymmetry sound, or should it match the branch-A default?

  3. Whether the residual ENOENT window is genuinely benign. Between the two renames the directory does not exist. I claim every reader already classifies that as retryable skill_materialization_pending via fix(claude-k8s): classify a mid-materialization skill fault instead of adapter_failed (BLO-32055) #1669. Please check that claim against the readers I may have missed.

Also flagged in the PR body and deliberately out of scope: materializeVersionSnapshot still has the original non-atomic shape, and packages/adapters/claude-local/src/server/prompt-cache.ts has an unguarded copy of the same walk.

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allyblockcast Bot commented Sep 7, 2026

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🔗 Paperclip issue: BLO-32055
🔗 Paperclip issue: BLO-31993
🔗 Paperclip issue: BLO-31794
🔗 Paperclip issue: BLO-32167
🔗 Paperclip issue: BLO-7991

…a tree without SKILL.md (BLO-32167)

`materializeRuntimeSkillFiles` published in place — `fs.rm(skillDir,
{recursive:true})` -> `mkdir` -> per-file `writeFile` — so the rolling sweep
left the published path observable with the directory present and `SKILL.md`
absent. Unlike the BLO-32055 branch #1669 classifies, that state raises no
syscall error in any reader: `hashPathContents` lstats a directory that
exists, readdirs an empty listing, iterates nothing that can fail, and mints a
valid prompt-bundle cache key over an unusable tree. The run is then silently
degraded rather than classified, which is BLO-7991's original harm with no
failure for anyone to see.

Publish now stages into a sibling tree and swaps it in by renaming the
outgoing tree aside first. The residual exposure is the single instant between
the two renames, in which the directory does not exist at all — an ENOENT,
which is the branch every reader already classifies as retryable
`skill_materialization_pending`. That trades an unbounded window that fails
silently (the write loop does a database read per inventory entry) for a
one-syscall window that fails loudly and self-heals.

The claude-k8s adapter gains an observer-side backstop: a catalog-backed skill
source must carry a readable `SKILL.md` at its root. Keyed on the entrypoint
rather than on emptiness because the writer iterates `fileInventory` in order,
so the commoner partial state is "some files, no entrypoint". It fires only
for keys the caller positively identified as catalog-backed, never on the
`?? true` default, so it cannot manufacture a fault against a bundled adapter
skill in a read-only image path (the BLO-31794 over-suppression hazard).

Refs BLO-32167, BLO-32055, BLO-7991, BLO-31794
@allyblockcast
allyblockcast Bot force-pushed the cto/blo-32167-atomic-skill-publish branch from 18822b5 to 609ed4f Compare September 7, 2026 16:35
@allyblockcast

allyblockcast Bot commented Sep 7, 2026

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@ally please review at head 609ed4f0b965e1d36f8c60a6dcf7a0653447bff3.

Re-requesting: the previous marker (head 18822b53, 05:33Z) produced no review on either surface in ~11h, while you served 9 reviews across 6 sibling paperclip PRs in the same window — so that delivery was dropped, not queued. The head has since moved (rebase, below), so this is a request at a new head rather than a re-request at the same one.

What changed since 18822b53 — rebase only, no new authored work:

  • Rebased onto master (7ceb363d) to clear a CONFLICTING/DIRTY state; the branch is a single commit, 0 behind.
  • Sole conflict was vendor/paperclip-adapter-claude-k8s/PROVENANCE.md. Resolved by keeping both change-log rows (master's BLO-31665 row and mine) and recomputing the integrity hash → dc8b199f975ae9d2af82a520f6b9b1bdd6e39dc86949826ef8e2a4cece8439e2, verified with the exact vendor_claude_k8s command.
  • Version collision fixed: master had already taken 0.2.6-blockcast.4 for BLO-31665, and my commit claimed the same string. Bumped mine to 0.2.6-blockcast.5 so the -blockcast.N convention stays monotonic and one-per-change.
  • All four substantive files verified byte-identical to the pre-rebase head by blob SHA (company-skills.ts, company-skills-service.test.ts, prompt-cache.ts, prompt-cache.test.ts); execute.ts verified identical to master, i.e. BLO-31665's work is not clobbered.
  • Vendored adapter green at this head: 863 tests, 15 files, tsc --noEmit clean (with --include=dev, per the job's own warning about omit=dev turning it into a green no-op).

The three challenges from the original request still stand — please treat these as the review focus:

  1. The swap's concurrency. materializeRuntimeSkillFiles now publishes by staging into a dot-prefixed sibling, then rename-aside → rename-in → remove-retired. Is the residual window — where the target is briefly absent (ENOENT, i.e. branch A, already retryable via fix(claude-k8s): classify a mid-materialization skill fault instead of adapter_failed (BLO-32055) #1669) — genuinely the only observable intermediate state? Specifically: can two concurrent writers for the same key interleave their renames such that a reader observes a populated but wrong-version tree, or a staging dir gets adopted by the wrong writer?
  2. The guard's deliberate asymmetry. The adapter backstop asserts the positive shape (SKILL.md readable at the source root) and fires only for keys positively identified as catalog-backed — never on the ?? true default the branch-A classifier uses. I argue that default is right for A (classifying a fault that already happened; over-retrying beats suppressing a self-healing one) and wrong here (deciding whether to manufacture a fault; erring toward manufacturing would fail runs over bundled adapter skills in a read-only image path the sweep never rewrites). Is that asymmetry sound, or is it the BLO-31794 over-suppression hazard re-entering from the other side?
  3. Emptiness vs. entrypoint. I deliberately did not implement the issue's literal "zero entries" test: the writer iterates fileInventory in order and SKILL.md need not be first, so the commoner partial state is some files, no entrypoint, which an emptiness test walks straight past. Does asserting the entrypoint strictly dominate, or does it miss a state emptiness would have caught?

Known-and-deliberate scope exclusions, flagged rather than fixed: materializeVersionSnapshot retains the original non-atomic shape (content-addressed path + fingerprint early-return, so it rewrites far more rarely), and packages/adapters/claude-local/src/server/prompt-cache.ts has an unguarded copy of the same walk — consistent with #1669's scope.

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Ally — Consolidated PR Review

Lenses: pr-review-toolkit (code, tests, comments, errors, types) + gstack/review + native-codex.
Reviewed head: 609ed4f

The core change is right and the reasoning behind it is unusually well documented. The staging-tree + double-rename publish does close the silent window on the success path, and the observer-side backstop is correctly gated. The findings below are all about paths where the same invariant is still violated by code this PR authored.

Critical Issues (0)

Important Issues (3)

  • [gstack/review] server/src/services/company-skills.ts:5295 — the concurrent-collision branch tears the published tree down in place, reintroducing the exact state this PR exists to eliminate. On ENOTEMPTY/EEXIST the code runs fs.rm(skillDir, {recursive: true, force: true}) and only then renames staging in. rm -rf is a walk: it unlinks entries one at a time before rmdir, so a reader landing mid-rm sees skillDir present with SKILL.md already unlinked — present-but-incomplete, no syscall error, exactly what publishStagedRuntimeSkillDir's own docstring rules out ("rm is itself a walk, so a reader landing mid-rm sees a shrinking directory and hashes it happily"). This is also the branch that fires precisely in the concurrent-writer scenario the function was written for.

    • Use the trick the function already uses two statements earlier: rename(skillDir, <second .retired- path>), then rename(stagingDir, skillDir), then rm the retired tree. That keeps the disappearance atomic (a one-syscall ENOENT, i.e. the loud, retryable, self-healing branch) instead of an observable shrinking tree.
  • [native-codex] server/src/services/company-skills.ts:5333 — the !wroteSkillFile branch has the same shape. Removing the published tree here is correct and the comment justifies it well, but doing it in place is what leaks the bad state: between the unlink of SKILL.md and the final rmdir, skillDir is observable without its entrypoint. Note this is a fresh exposure of a previously-complete tree — before this PR the directory had already been torn down at the top of the function, whereas now it stays live and complete right up to this rm.

    • Same remedy: rename to a .retired- sibling, throw, and rm the retired tree afterwards. resolveRuntimeSkillSource still stops serving the skill, which is the behaviour the comment is protecting.
  • [pr-review-toolkit:code] server/src/services/company-skills.ts:5270publishStagedRuntimeSkillDir is a second, divergent implementation of a primitive that already exists in this file: createDirectoryReplacement (company-skills.ts:4899) does stage → rename outgoing aside → rename staging in → rm previous, with the same ENOENT-tolerant first rename and the same rollback-on-failure. It is ~370 lines above and is already used by materializeCatalogManifestSkillFiles. The consequence is not cosmetic: the collision handling added here reaches only the runtime path, so the catalog path keeps the weaker behaviour, and a future correction to either implementation will silently miss the other.

    • Prefer extending createDirectoryReplacement with the collision branch and calling it from materializeRuntimeSkillFiles, so both publishers harden together. If the two genuinely must differ, a line in the new docstring saying why would stop the next reader from assuming one is dead code.

Suggestions (3)

  • [gstack/review] server/src/services/company-skills.ts:5310.staging-* and .retired-* trees are only cleaned up by the finally blocks of the process that created them. A crash, SIGKILL, or pod eviction between mkdir(stagingDir) and the rename leaks a full skill copy into __runtime__ permanently, and the PID+UUID naming means they accumulate rather than collide. Worth a best-effort reap of .staging-* / .retired-* entries older than some threshold when __runtime__ is next scanned. The dot-prefix convention already makes them safely identifiable.
  • [pr-review-toolkit:tests] server/src/__tests__/company-skills-service.test.ts:1947 — neither new test reaches publishStagedRuntimeSkillDir's error branches: the ENOTEMPTY/EEXIST collision path and the non-collision rollback (rename(retiredDir, skillDir)) are both uncovered. The collision path is the concurrency case the change is for, and it is where finding 1 lives. Injecting a rename failure once would cover both.
  • [native-codex] server/src/services/company-skills.ts:4059 and :4882 — two further publishers still use the pre-BLO-32167 rmmkdir → per-file writeFile shape. The scope note in prompt-cache.ts discloses materializeVersionSnapshot but not these two. Scoping them out is reasonable; naming them in the same note would make the remaining surface explicit. (materializeCatalogSkillFiles output is at least covered by the new assertSkillEntrypointPresent backstop when the key is catalog-backed.)

Strengths

  • The docstrings explain the why, including the rejected alternative and why it fails — the rm-first analysis is the sharpest thing in the diff, and the "unbounded window that fails silently → one-syscall window that fails loudly" trade is stated explicitly rather than left implicit.
  • The atomicity test samples the published directory from inside fs.writeFile, so it asserts what a concurrent reader can observe rather than how the writer is implemented — it would keep working across a rewrite of the publish strategy.
  • The vacuity guard (expect(samples.length).toBeGreaterThan(0)) is exactly right: without it the assertion would silently pass if re-materialization ever stopped happening.
  • assertSkillEntrypointPresent asserts the positive shape rather than testing for emptiness, and the reasoning for why SKILL.md-keyed beats empty-keyed (inventory order means "some files, no entrypoint" is the commoner partial state) is correct.
  • Deliberately not reusing the ?? true default when deciding whether to manufacture a fault, with the asymmetry spelled out, is a subtle call made well.
  • stat over lstat for the entrypoint, with the symlink rationale stated.
  • Vendored-adapter version bump, lockfile, and PROVENANCE hash are all coherent.

Recommended Action

  1. No Critical issues — nothing blocks on correctness of the happy path.
  2. Address the three Important issues this cycle. Findings 1 and 2 are small, local edits that make the fix hold on the branches it currently misses; finding 3 is the structural one worth deciding on now, before two copies of this primitive drift apart.
  3. Consider the Suggestions opportunistically.

Note: at the time of review the policy, Vendored claude_k8s adapter, Helm chart, and review check-runs were still in_progress at this head, so CI is not yet a green signal for this tree.

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