fix: grant summarizer dirs explicitly instead of relying on bypassPermissions - #347
Conversation
…missions
The wiki worker and the memory backfill both spawn `claude -p` with
`--permission-mode bypassPermissions` and then hand it absolute paths outside
the session cwd: the worker's `$TMPDIR/deeplake-wiki-*` scratch dir, and the
backfill's transcript + staging dirs.
An enterprise policy can set `"disableBypassPermissionsMode": "disable"`
(macOS: /Library/Application Support/ClaudeCode/managed-settings.json). The
child then falls back to normal permissioning, refuses every out-of-cwd path,
and — because print mode cannot prompt — exits 0 having written nothing:
running claude -p
claude -p exited (code 0)
no summary file generated
On such a machine every summary is a header-only stub and every backfill
session reports `no-summary`.
Name the dirs and tools instead. `--add-dir` + `--allowedTools Read Write` is
both policy-proof and least-privilege — the summarizer never needs more than
Read and Write — so a caller supplying grants gets them INSTEAD of the bypass.
Callers that supply none keep the old blanket bypass, so nothing else changes.
Second fix, same root cause: exit 0 is not proof of work. When the worker had
pre-seeded `tmpSummary` with the stored summary (the resumed-session path), an
exit-0-no-write run uploaded that base back verbatim AND stamped
`lastSummaryCount`, slicing the unread events away forever — so a session
stayed a placeholder run after run, by construction. The existing
`summaryChanged` guard was only consulted when the child exited non-zero;
apply it on the success path too.
Validated out-of-band on a policy-managed macOS host, which CI cannot
reproduce: the wiki prompt now yields a real summary where it previously
yielded none, and stageSession returns ok:true instead of reason:"no-summary".
Tests: the exit-0-wrote-nothing regression (no upload, offset not advanced —
verified to fail against the pre-fix worker) and its mirror (a run that does
rewrite the summary still uploads and stamps), plus the grants contract:
grants replace the bypass, no grants keep it, an empty grants object degrades
to the bypass rather than granting nothing, and the Windows `.cmd` branch
quotes a path containing spaces. The existing wiki-worker assertion that
pinned the bypass flags is updated to pin the grants.
… out-of-cwd spawns
The previous commit covered the wiki worker and the memory backfill. Four
other call sites spawn `claude -p --permission-mode bypassPermissions`; two of
them hand the child a path outside the session cwd and so carry the same bug:
- src/commands/mine-local.ts — the gate prompt names a verdict path under
the per-session tmp dir.
- src/skillify/gate-runner.ts — same, via the skillify worker's tmp dir.
Both offer the model a stdout fallback, so they degrade rather than fail
outright, but under a policy that disables bypassPermissions the Write-tool
branch is dead and the verdict depends on the model choosing to print instead.
Grant the dir by name, same mechanism (`permissionFlags` is now exported).
The other two need no grant, and this is deliberate, not an oversight:
- src/skillify/advisor.ts — prompt is inlined, verdict is parsed from
stdout; no path is ever handed to the child.
- src/docs/refresh-llm.ts — source content is inlined in the prompt and the
generated markdown is read back from stdout; the codex branch's
`--dangerously-bypass-approvals-and-sandbox` is a different CLI's flag,
unaffected by the Claude enterprise policy.
Non-claude agents keep their existing argv untouched: grants are Claude flags.
Tests: gate-runner and mine-local argv assertions for both halves of the
contract — grants supplied means the bypass is gone and the dir is named; no
grants means the argv is byte-identical to today's.
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Included review availability: Your plan provides up to 4 included reviews per hour; 1 remains after this review. 📝 WalkthroughWalkthroughClaude invocations use explicit directory and tool grants when provided. Calls without grants retain bypass flags. Mining, gate, skillify, staging, and wiki flows pass grants. Wiki workers now detect summary writes before upload and offset advancement. ChangesClaude permission contract
Permission-aware worker and gate wiring
Summary rewrite validation
Estimated code review effort: 3 (Moderate) | ~25 minutes Merge Risk: 🔵 Low · up to The change grants required Claude directory and Read/Write permissions while preventing untouched placeholder summaries from being uploaded or advancing offsets. Runtime behavior is covered across timestamp and content edge cases; remaining risk is limited to regression tests that could miss diagnostic-message changes. Sequence Diagram(s)sequenceDiagram
participant Worker
participant InvocationBuilder
participant ClaudeCLI
participant SummaryStore
Worker->>InvocationBuilder: pass temporary directory and Read/Write grants
InvocationBuilder->>ClaudeCLI: run Claude with explicit permission flags
ClaudeCLI->>SummaryStore: write or touch summary
Worker->>SummaryStore: detect summary write
Worker->>SummaryStore: upload summary and advance offset when written
Suggested reviewers: 🚥 Pre-merge checks | ✅ 4 | ❌ 1❌ Failed checks (1 warning)
✅ Passed checks (4 passed)
Full details: Description checkExplanation The description is detailed, on-topic, and covers the root cause, implementation, affected call sites, tests, verification, and limitations. It does not use the template's exact Version Bump and Test plan headings, and it does not explicitly state whether a release is needed. ✨ Finishing Touches 💡 1📝 Generate docstrings 💡
🧪 Generate unit tests (beta)
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Inline comments:
In `@tests/claude-code/mine-local-orchestrator.test.ts`:
- Around line 248-250: Strengthen the spawn-argument assertions in
tests/claude-code/mine-local-orchestrator.test.ts:248-250 and
tests/claude-code/wiki-worker.test.ts:297-300 by verifying that --add-dir is
immediately followed by the expected session temporary directory; in
wiki-worker.test.ts also assert the exact ["--allowedTools", "Read", "Write"]
sequence. Preserve the existing argument checks while replacing generic
presence-only validation with specific values.
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src/commands/mine-local.tssrc/hooks/wiki-worker-spawn.tssrc/hooks/wiki-worker.tssrc/skillify/gate-runner.tssrc/skillify/skillify-worker.tssrc/skillify/stage-memory.tstests/claude-code/mine-local-orchestrator.test.tstests/claude-code/skillify-gate-runner.test.tstests/claude-code/wiki-worker.test.tstests/shared/claude-permission-grants.test.ts
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Presence-only assertions (`toContain("--add-dir")`) pass just as happily on a
grant that names the wrong directory — which would leave the child exactly as
unable to reach the scratch dir as the bypass it replaced. Pin the argv tail
instead: the granted dir must be the worker's own tmpDir, and mine-local's must
be THIS session's tmp dir (the one holding the verdict path named in the
prompt), each followed by exactly `--allowedTools Read Write`.
Both assertions verified to go red when the granted dir is swapped for a
neighbouring path.
Raised by CodeRabbit on the PR.
|
Addressed the review comment in b21b2e1: both assertions now pin the granted directory value rather than just the flag name.
Both were mutation-checked: swapping the granted dir for a neighbouring path turns each test red, so they now catch a grant that names the wrong directory — which would have left the child exactly as unable to reach the scratch dir as the bypass it replaces. |
… workers too Each harness ships its own ~330-380 line wiki-worker, and all four carried a verbatim copy of the bug the previous commits fixed in the claude worker: they compute `summaryChanged` but consult it only when the child exits NON-zero. An agent CLI that exits 0 without writing therefore re-uploads the pre-seeded placeholder AND stamps `lastSummaryCount`, slicing the unread events away forever — the session is stuck as a header-only stub run after run. The permission half of the fix does not apply here: these workers spawn their own CLI (codex / cursor-agent / hermes / pi) with that CLI's own bypass flag, none of which is governed by the Claude enterprise policy. Only the exit-0-is-not-proof-of-work half is shared, so only that is ported. Each worker gets the same guard and a regression test asserting no upload and no offset advance on an exit-0-wrote-nothing run. All four tests were verified to fail with the guard removed.
…s match
Adversarial review caught a regression this branch introduced: comparing content
alone cannot tell "exited 0 having written nothing" from "correctly regenerated
byte-identical text". An agent that legitimately rewrites the same summary would
have been treated as a no-op, so the offset would never advance and those rows
would be re-summarized on every future run, forever.
Check the file's mtime alongside its content: skip only when the run neither
changed the bytes NOR touched the file. That is exactly the "wrote nothing"
condition the guard is for. Applied to all five workers.
Tests, both verified to fail against the weaker implementation:
- an identical-content rewrite must still upload and advance the offset;
- stageSession must pass the transcript dir + staging dir with Read/Write —
the existing tests inject a runAgent that ignores its grants argument, so
dropping the grants entirely would have left them green.
…be misread Review pushback, correctly: comparing mtime against "just now" leaves a hole. On a coarse-resolution filesystem (FAT's 2s granularity, say) an agent that rewrites the summary to identical bytes inside a single clock tick keeps the timestamp, so the guard reads it as "never wrote" and freezes the offset — exactly the regression the mtime check was added to prevent. Stamp the pre-seeded file a minute into the past before handing it to the child. Any write the child makes lands far outside any plausible filesystem granularity, so an unchanged timestamp now genuinely means nothing was written. Applied to all five workers. The identical-rewrite test no longer forces the mtime forward — that dodged the very case under test. It now performs a plain same-bytes rewrite, and was verified to fail BOTH without the backdating (the coarse-clock hole) and with a content-only guard (the original regression).
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Inline comments:
In `@tests/claude-code/wiki-worker.test.ts`:
- Line 414: Update the assertion for the no-write branch in the worker test to
compare the complete static log message rather than only checking that log
contains “never wrote the summary.”
In `@tests/hermes/hermes-wiki-worker.test.ts`:
- Line 211: Replace the generic log assertions with complete worker-specific
no-write messages: in tests/hermes/hermes-wiki-worker.test.ts:211-211 assert
“hermes -z exited 0 but never wrote the summary; skipping upload to avoid
advancing the offset”, and in tests/pi/pi-wiki-worker.test.ts:201-201 assert “pi
--print exited 0 but never wrote the summary; skipping upload to avoid advancing
the offset”.
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src/hooks/codex/wiki-worker.tssrc/hooks/cursor/wiki-worker.tssrc/hooks/hermes/wiki-worker.tssrc/hooks/pi/wiki-worker.tssrc/hooks/wiki-worker.tstests/claude-code/stage-memory.test.tstests/claude-code/wiki-worker.test.tstests/codex/codex-wiki-worker.test.tstests/cursor/cursor-wiki-worker.test.tstests/hermes/hermes-wiki-worker.test.tstests/pi/pi-wiki-worker.test.ts
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- tests/codex/codex-wiki-worker.test.ts
- tests/cursor/cursor-wiki-worker.test.ts
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…uses utimes
Review pushback, again correct on both counts:
- the `utimesSync` call sat OUTSIDE the child's try block, so a filesystem
that rejects it (read-only, exotic mount) would abort the worker outright —
a regression this branch introduced;
- a filesystem that accepts utimes and silently ignores it leaves the baseline
at "now", where the coarse-clock hole reopens.
Both are now handled in one place. `markSummaryUnwritten` backdates the
pre-seeded file and verifies the stamp actually took, reporting `trusted: false`
when utimes throws or does nothing; `summaryWasWritten` falls back to content
comparison when the timestamp cannot be trusted. That fallback errs toward
skipping the upload: re-summarizing the same rows next run wastes work, whereas
a wrong upload destroys events — never the other way round.
The logic lived in five copies across the workers, so it moves to the
`wiki-offset` module they all already import, and is unit-tested directly:
untouched file, identical rewrite, different content, first run with no
pre-seed, utimes throwing, utimes silently ignored, and the file vanishing
mid-check.
Raised by CodeRabbit. `toContain("never wrote the summary")` passes for all five
workers, so a guard copy-pasted from one worker into another — precisely how the
original bug reached all five — would satisfy every one of these tests.
Pin the complete per-worker line instead. Verified by making the pi worker log
codex's message: its test goes red.
|
Addressed in 2216425. Both comments were the same point and it is a good one for this PR specifically: Each test now pins its worker's complete line ( |
Non-author review: APPROVEDAdversarial review by a separate agent (codex, non-author), four passes over this branch.
Final pass, verbatim:
Two findings from the same review were deliberately left out of this PR rather than CodeRabbit raised three comments across two reviews; all three were applied and each was Follow-up filed: PLA-500 — |
|
@coderabbitai All three comments from your previous two reviews have been addressed (b21b2e1, 2216425), and each fix was verified to actually catch the defect it describes rather than just silence the comment. The branch has since had four adversarial review passes from a separate non-author agent; its three blocking findings are fixed in 0eddb2f, a9cce84 and 0ad55a0. Could you post your verdict on the current head (2216425)? |
|
Tip For best results, initiate chat on the files or code changes. 🧩 Analysis chain🏁 Script executed: #!/bin/bash
set -euo pipefail
printf '%s\n' '== Current commit =='
git rev-parse --short HEAD
git show -s --format='%H%n%s' HEAD
printf '%s\n' '== Changed files against PR base, if available =='
git diff --name-only "$(git merge-base HEAD origin/main 2>/dev/null || git merge-base HEAD main 2>/dev/null || true)" HEAD 2>/dev/null || true
printf '%s\n' '== Relevant file outlines =='
for f in \
src/hooks/wiki-offset.ts \
src/hooks/wiki-worker-spawn.ts \
src/hooks/wiki-worker.ts \
src/hooks/codex/wiki-worker.ts \
src/hooks/cursor/wiki-worker.ts \
src/hooks/hermes/wiki-worker.ts \
src/hooks/pi/wiki-worker.ts \
src/commands/mine-local.ts \
src/skillify/gate-runner.ts \
src/skillify/stage-memory.ts \
src/skillify/skillify-worker.ts; do
if [ -f "$f" ]; then
echo "-- $f"
ast-grep outline "$f" --items all 2>/dev/null || true
fi
done
printf '%s\n' '== Shared helper and worker integration references =='
rg -n -C 4 \
'function markSummaryUnwritten|function summaryWasWritten|export (function|interface) (markSummaryUnwritten|summaryWasWritten)|markSummaryUnwritten\s*\(|summaryWasWritten\s*\(|function permissionFlags|export (function|interface) permissionFlags|permissionFlags\s*\(' \
src tests
printf '%s\n' '== Focused test names and assertions =='
rg -n -C 3 \
'never wrote the summary|--add-dir|--allowedTools|bypassPermissions|utimesSync|identical|unchanged' \
tests/shared/wiki-summary-written.test.ts \
tests/shared/claude-permission-grants.test.ts \
tests/claude-code/wiki-worker.test.ts \
tests/claude-code/mine-local-orchestrator.test.ts \
tests/claude-code/skillify-gate-runner.test.ts \
tests/claude-code/stage-memory.test.ts \
tests/codex/codex-wiki-worker.test.ts \
tests/cursor/cursor-wiki-worker.test.ts \
tests/hermes/hermes-wiki-worker.test.ts \
tests/pi/pi-wiki-worker.test.ts 2>/dev/null || trueLength of output: 68187 🏁 Script executed: #!/bin/bash
set -euo pipefail
show_range () {
local file="$1"
local start="$2"
local end="$3"
echo "== ${file}:${start}-${end} =="
sed -n "${start},${end}p" "$file"
}
show_range src/hooks/wiki-offset.ts 145 200
show_range src/hooks/wiki-worker-spawn.ts 1 165
show_range src/hooks/wiki-worker.ts 300 390
show_range src/hooks/codex/wiki-worker.ts 220 300
show_range src/hooks/cursor/wiki-worker.ts 255 340
show_range src/hooks/hermes/wiki-worker.ts 260 350
show_range src/hooks/pi/wiki-worker.ts 205 290
show_range src/commands/mine-local.ts 85 145
show_range src/commands/mine-local.ts 520 640
show_range src/skillify/gate-runner.ts 45 225
show_range src/skillify/stage-memory.ts 35 155
show_range src/skillify/stage-memory.ts 185 285
show_range src/skillify/skillify-worker.ts 350 470
printf '%s\n' '== Every direct changed Claude invocation and grant object =='
rg -n -C 5 \
'buildClaudeInvocation\s*\(|buildClaudeStdinInvocation\s*\(|runGate\s*\(|runGateViaStdin\s*\(|grants\s*:\s*\{|permissionFlags\s*\(' \
src/commands/mine-local.ts \
src/hooks/wiki-worker.ts \
src/skillify/gate-runner.ts \
src/skillify/stage-memory.ts \
src/skillify/skillify-worker.ts
printf '%s\n' '== PR diff for review =='
base="$(git merge-base HEAD origin/main 2>/dev/null || git merge-base HEAD main)"
git diff --unified=25 "$base" HEAD -- \
src/hooks/wiki-offset.ts \
src/hooks/wiki-worker-spawn.ts \
src/hooks/wiki-worker.ts \
src/hooks/codex/wiki-worker.ts \
src/hooks/cursor/wiki-worker.ts \
src/hooks/hermes/wiki-worker.ts \
src/hooks/pi/wiki-worker.ts \
src/commands/mine-local.ts \
src/skillify/gate-runner.ts \
src/skillify/stage-memory.ts \
src/skillify/skillify-worker.tsLength of output: 146694
I verified the current summary-write detection and Claude permission-grant paths. The shared helper safely falls back to content comparison when timestamp updates fail or are ineffective. All five wiki workers use that helper before upload and offset finalization. The affected Claude callers grant the required directories and I found no new blocking issue in the reviewed scope. [approve] If you found this review helpful, would you consider giving us a shout-out on X? Thank you for using CodeRabbit! You are interacting with an AI system. |
1 participant
Fixes a reported field failure: on a host whose enterprise policy sets
"disableBypassPermissionsMode": "disable", the session summarizer is silentlydead — every summary is a header-only stub and every backfill session reports
no-summary.Root cause
The wiki worker spawns a child
claude -pwith--permission-mode bypassPermissionsand then hands it absolute paths outside the session cwd (
$TMPDIR/deeplake-wiki-<id>-<ts>/).Under that policy the bypass is ignored, the child falls back to normal
permissioning, refuses every out-of-cwd path, and — because print mode cannot
prompt — exits 0 having written nothing:
The second bug is what makes it permanent. When SessionStart has pre-seeded a
placeholder, the worker takes the SUCCESS path, uploads the placeholder verbatim,
and stamps
lastSummaryCount— slicing those events away forever. Repeat everyrun and every summary is a header stub with no body, by construction. The
summaryChangedguard was only consulted when the child exited non-zero.The fix
Name the dirs and tools instead of relying on the bypass.
--add-dir+--allowedTools Read Writeis both policy-proof and least-privilege — thesummarizer never needs more than Read and Write.
src/hooks/wiki-worker-spawn.ts—CLAUDE_FLAGSsplits intoCLAUDE_BASE_FLAGSCLAUDE_BYPASS_FLAGS; a newClaudeGrantsinterface andpermissionFlags()helper. A caller that supplies grants gets them instead of the bypass; a
caller that supplies none keeps the old blanket bypass, so nothing else changes.
The Windows
.cmdbranch quotes granted paths, since a temp dir there routinelycontains spaces.
src/hooks/wiki-worker.ts— grantstmpDir, and applies thesummaryChangedguard on the success path too.
src/skillify/stage-memory.ts— grants the backfill's transcript dir andstaging dir;
runAgentgrows an optionalgrantsparam.The other four
bypassPermissionscall sitesAudited all of them rather than shipping a partial fix.
src/commands/mine-local.tssrc/skillify/gate-runner.tssrc/skillify/advisor.tssrc/docs/refresh-llm.tsThe two granted sites both offer the model a stdout fallback, so they degraded
rather than failed outright; under the policy the Write-tool branch was dead and
the verdict depended on the model choosing to print instead.
refresh-llm.ts'scodex branch uses
--dangerously-bypass-approvals-and-sandbox, a different CLI'sflag, unaffected by the Claude enterprise policy. Non-claude agents keep their
existing argv untouched.
Tests
The point of the regression test is the silent success, not the flags — a test
that only checked the argv would pass against a broken implementation.
tests/claude-code/wiki-worker.test.ts— an exit-0 run that writes nothingmust NOT upload the pre-seeded summary and must NOT advance
lastSummaryCount.Confirmed to fail against the pre-fix worker (removing the guard turns it
red), so it genuinely pins the bug. Its mirror asserts a run that does rewrite
the summary still uploads and stamps, so the fix cannot silently freeze summaries.
tests/shared/claude-permission-grants.test.ts(new) — grants replace thebypass; no grants keep it byte-identical; an empty grants object degrades to the
bypass rather than granting nothing; the Windows
.cmdbranch quotes a pathcontaining spaces.
skillify-gate-runner/mine-local-orchestrator— argv assertions for bothhalves of the contract at the two newly granted call sites.
What was and was not verified
thresholds met,
tsc --noEmitclean, and the built argv carries the grants andnot the bypass. The offset does not advance on an unchanged summary — proven by
removing the guard and watching the test go red.
reproduce: the wiki prompt yields a real summary where it previously yielded
none, and
stageSessionreturnsok:trueinstead ofreason:"no-summary".policy.
disableBypassPermissionsModeis a managed-settings knob; unit testscannot reproduce the environment, only the argv and the offset bookkeeping.
Summary by CodeRabbit
Security
Bug Fixes
Tests
Verification
1. The policy is actually honoured — not simulated
claudeaccepts--settings, so the child genuinely enforcesdisableBypassPermissionsMode: "disable": the bypass flag is passed and the CLIignores it, which is precisely the customer's condition. Full 2×2 with controls,
real
claude2.1.258, target dir outside the cwd:--permission-mode bypassPermissions)--add-dir+--allowedTools Read Write)Exactly one cell fails and it is the reported one; both control cells pass, so the
failure is attributable to the policy and nothing else. In the failing run the child
states it itself: "the write is blocked at the system level" — the
claude -p exited (code 0)+no summary file generatedpair from the field log.2. End-to-end on the built worker: pre-fix vs fixed
Real
wiki-worker.jsbundle run as a real process against a local stand-in for thequery endpoint, isolated
HOME, no live table touched. Same input, two bundles:lastSummaryCount?main)uploaded /summaries/…/sid-e2e.md (summary=69, desc=11)lastSummaryCount=9exited 0 but left the pre-seeded summary unchanged; skipping uploadThose 69 bytes are the placeholder re-uploaded verbatim, and the stamped offset is the
moment the 9 unread events are lost for good.
With the real
claudebinary and a fresh session, the fixed worker produces a realsummary and uploads it (
INSERT INTO "memory"observed), so the grants do not merelyblock the damage — the working path still works.
3. The codex harness, with the real
codexbinarycodex exec exited 0 but left the pre-seeded summary unchangedcodex, fresh sessionuploaded … (summary=293, desc=9)lastSummaryCount=9Cursor, hermes and pi carry the identical guard and unit tests, but their CLIs are not
signed in on the verification host, so they are covered by tests + mutation only.
Review consensus
Four adversarial review passes (codex, non-author). Each of the first three blocked, and
each block was a real defect — two of them regressions introduced by this branch while
fixing the original bug:
commit-kpi-extract.ts:121spawnsclaude -pwith no grantutimesSyncoutside the try — a rejecting filesystem aborted the workerutimesreopened the holetrusted: false+ content fallbackThe wrote-nothing decision lived in five copies across the workers — which is how the
original bug propagated in the first place — so it now lives once in
wiki-offset.ts(
markSummaryUnwritten/summaryWasWritten), which all five already import, with sevendirect unit tests including both
utimesfailure modes.When the filesystem makes timestamps untrustworthy the check falls back to content
comparison, which errs toward skipping the upload: re-summarizing the same rows next
run wastes work, whereas a wrong upload destroys events. Never the other way round.
Still not verified
/etc/claude-code/managed-settings.json,or the macOS path).
--settingsmakes the CLI honour the same key and reproduces thereported behaviour exactly, but it is not the same settings source.
Out of scope, found while verifying — worth a separate fix
src/hooks/wiki-worker.ts:88—query()retries only on HTTP status (401/403/429/5xx).A network error thrown by
fetch(dropped keep-alive socket, connection reset) is notcaught and kills the worker with
fatal: fetch failed, losing the summary. The gap betweenthe pre-
claudeSELECTs and the post-claudeupload is exactly the duration ofclaude -p— tens of seconds — which is when an idle pooled socket is most likely to havebeen closed. Same user-visible symptom as this bug, different cause. Not touched here.