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fix: harden the stall defect class found auditing the 1.2.2 fix - #392

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fix/stall-class-hardening
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fix: harden the stall defect class found auditing the 1.2.2 fix#392
gloryfromca merged 17 commits into
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fix/stall-class-hardening

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@gloryfromca gloryfromca commented Aug 5, 2026

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Audit follow-up to #384 / #386. The version-cleanup stall those fixed had a shape worth generalising: an unbounded await in a path whose scheduler treats "not finished" as "skip" — so one hang stops that work forever, and because nothing failed, every health signal built from failure counters reads as healthy.

Seven instances were found. Five are fixed here; the reasoning for what is deferred is at the bottom.

What each fix addresses

Defect Consequence if hit Evidence grade
5 read ops had no deadline whole md → LanceDB projection stops; rows stuck in processing; /health green never observed in ~120h of soak
heartbeat / rebuild loops had no outer try that loop dies permanently, zero log output not observed; reachable only via create_task on a closing loop
fallback rebuild reset the alert counter optimize_failure_streak >= 5 unreachable (~1% observable) logic certain; the triggering condition never observed
husk sweep relied on a lock it cannot hold table left with no FTS index → that kind's searches 500 three-way race, very low
memory-root lock wait unbounded + silent startup looks like a hang with no explanation not observed

None is high-probability. What they share with the fixed bug is the shape, and one of them (reads) has a strictly larger blast radius than the original — it stops all projection, not one table's cleanup.

Notable reasoning

Reads were deliberately skipped last round on the grounds that a read takes no lock and so blocks no writer. That is true and was the wrong conclusion: the drain loop reads on every batch and advances one batch at a time, so a hung read parks the pipeline even though it parks no lock.

The husk sweep's docstring contract was unsatisfiable. It required the write lock, but the sweep runs via asyncio.to_thread and a deadline cancels the future, not the thread — so an orphan sweep outlives any critical section, and Path.iterdir is a lazy os.scandir that can yield a dir created after the scan began. Holding the lock harder does not fix it; an age filter (skip dirs younger than lance's own 7-day unverified threshold) holds regardless of lock ownership, so that is the guarantee now.

The lock wait was made pollable rather than merely bounded. Wrapping a blocking flock in a timeout is worse than no timeout: cancelling the coroutine leaves the worker thread to acquire the lock later with nobody left to release it. Short LOCK_NB attempts on an interval give the same semantics while being bounded and cancellable.

Loop supervision escalates to process exit (SIGTERM, so the ASGI server shuts down gracefully) after 5s/15s/45s restarts. This assumes a restarting supervisor; without one the process stops, which still beats serving searches from a silently frozen index.

Verification

  • 1925 unit + 182 integration passing; ruff clean; import-linter 3/3 contracts kept.
  • Mutation-verified — each fix reverted individually, confirming the new test turns red rather than merely passing alongside it:
Reverted to Test outcome
table handle outside the read deadline hangs (the defect's actual signature)
husk sweep back inside the write lock fail
age floor set to 0 fail
restart budget removed fail
process-exit request removed fail
alert counter reset restored fail
waiting log removed fail

Deferred, with reasons

  • Rebuild starvation — the optimize runner's loop condition is "while there is unindexed data", which under sustained writes is never, so the 12h rebuild sweep waits it out. The 180s bound here makes that visible (cascade_lancedb_rebuild_skipped_optimize_unfinished) but not absent. The functional fix needs the runner to yield when a rebuild is pending, which changes the optimize↔rebuild mutual-exclusion contract — both commit on the same manifest version, so getting it wrong is worse than the bug. It also cannot be validated today: the cadence is 12h and no soak run has exceeded 2h, so the periodic sweep has only ever run at boot (where there is no write load). Making the cadence configurable is a prerequisite.
  • OME config hot-reload (awatch outside its try) — only the optional OME subsystem's hot reload dies; running config is unaffected and a restart clears it.
  • Progress clocks in /health — five of the seven are invisible because the verdict is assembled from failure counters, which a hang leaves untouched. last_prune_at is the one exception and is the only reason the original bug was ever found. Giving each long-lived loop a last-success clock is the structural fix; the drain half is nearly free, since max_lsn / last_processed_lsn are already computed and then dropped when building CascadeHealth.

Review follow-up (adversarial pass)

Four findings from the adversarial review, fixed on this branch (each with a mutation-verified test where applicable):

  • Supervisor restart budget is now per incident, not per process lifetime — a body that ran 60s+ before crashing gets the full ladder back, so independent transients days apart cannot pool into a SIGTERM.
  • A husk-sweep timeout no longer fails prune() — the cleanup commit has already succeeded at that point; letting the best-effort sweep's deadline escape counted a prune "failure" and stalled the prune-staleness clock for a stall that did not happen. Reachable at ceiling-load steady state, where sweep time sits right at the 60s budget.
  • The husk reclaim horizon is ~14 days, not 7 — POSIX bumps a dir's mtime when the cleanup empties it, so the age gate restarts then; docstring numbers corrected to ~1.8M dirs / ~7GB at ceiling (the "never more aggressive than lance" property is unaffected).
  • Memory-root lock default raised to 30min — 300s sat at the edge of the legitimate hold; the bound's job is diagnosis (the wait is already logged), so it now sits an order of magnitude above, and the timeout message points at the still-alive holder.

🤖 Generated with Claude Code

zhanghui and others added 6 commits August 5, 2026 13:55
Two instances of the same defect class the write-lock deadline work left
behind: an await in a scheduler-gated path with nothing bounding it.

Reads (count / get_by_id / find_where / find_where_paginated / search) were
skipped last round on the reasoning that a read takes no lock and so blocks
no writer. True, but incomplete: the cascade drain loop reads on every batch
and advances strictly one batch at a time, so a read that never returns stops
the whole md -> LanceDB projection. Claimed rows stay `processing` forever
(claim_pending_batch only takes `pending`, orphan recovery runs once at
startup), and /health keeps reporting healthy because a hang raises nothing.
Budget 60s, ~1000x the measured 62ms flat scan over 117k rows.

The empty-index-dir sweep ran inside the prune critical section under a
docstring contract requiring the write lock. That contract could not hold: the
sweep runs via asyncio.to_thread, and a deadline cancels the future, not the
thread, so an orphan sweep outlives the lock -- and Path.iterdir is a lazy
os.scandir, so it can yield a dir created after the scan began. It could
therefore rmdir a directory a concurrent create_index had just made, leaving
the table with no FTS index and every search on that kind 500ing. Safety now
comes from an age filter (skip dirs younger than 300s), which holds regardless
of lock ownership; the sweep moved out of the critical section so a slow
filesystem walk can no longer overrun the prune budget.

Mutation-verified: moving the table handle back outside the read deadline
hangs the new test; moving the sweep back inside the lock fails it; setting
the age floor to 0 fails the fresh-dir test.

Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
The drain / heartbeat / rebuild loops were plain create_task coroutines. One
uncaught exception ended that loop permanently: nothing restarted it, and
because the worker holds a strong reference to the task the interpreter never
printed "Task exception was never retrieved" either (that fires on GC). The
loop's job just stopped happening with zero output. _run_loop had an inner
try; its two siblings did not.

Each loop now runs under _supervise: log, wait, restart with escalating
backoff (5s / 15s / 45s), then request process exit via SIGTERM so a
restarting supervisor (systemd Restart=always, Docker restart:
unless-stopped, a k8s Deployment) can recover it. SIGTERM rather than
os._exit so the ASGI server runs its graceful-shutdown path. A done-callback
is the last-resort observer for the supervisor itself ending unexpectedly.

Separately, the fallback rebuild reset the same counter the health verdict
reads, so the optimize-failure threshold was effectively unreachable: a table
failing 100% of the time cycled 1..5 -> 0 -> 1.. and the threshold value
existed only during the sub-second rebuild, ~1% observable against a 30s
scrape. cascade.healthy stayed green while the table never reclaimed a
version. The rate limiter moves to failures_since_fallback; only a successful
optimize clears the alert streak. Same shape as the run7 cross-kind max()
masking bug -- a remediation path refreshing the signal meant to report it.

Mutation-verified: dropping the restart budget, removing the exit request,
and restoring the counter reset each turn the corresponding test red.

Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
Acquisition polls with LOCK_NB instead of blocking inside a worker thread. A
blocking flock could be neither bounded nor cancelled: cancelling the awaiting
coroutine leaves the thread to acquire the lock later with nobody left to
release it, which is strictly worse than waiting.

The wait itself is correct by design -- the second process is supposed to wait,
then find the migration already done -- and flock is released by the kernel on
process exit, so a dead holder never wedges it. What was wrong is that it had
no upper bound and emitted nothing: a server startup landing on a held lock
looked like a hang whose last log line was lifespan_provider_startup
name=lancedb. It now logs memory_root_lock_waiting on first contention,
reports how long it waited on success, and gives up after timeout_seconds
(default 300s, generous because the legitimate holder is an O(rows) migration).

Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
test_lap_append_during_handler_no_loss asserted no loss after
_wait_path_done, whose settle window is 0.1s. That is a bet that the
filesystem event for the appends which landed *during* a handler
invocation has already been delivered — a terminal row does not mean the
file is fully projected, because the handler read the md at whatever
length it had then, marked the row done, and the rest arrive on a later
event. The bet holds on macOS/fsevents and lost on a loaded Linux runner
(md=30 lance=17), failing the assertion for a reason unrelated to the
behaviour under test.

Waits for quiescence instead: terminal row + empty pending queue + a
projected count unchanged across three consecutive polls. Strictly
stronger than the old condition, and real loss still fails — the count
just converges below the md entry count and stays there.

Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
rebuild_indexes dropped every index and recreated it. The docstring justified
that with "LanceDB transparently falls back to brute-force scan", which is true
for vector search and false for FTS: with no inverted index a BM25 query raises
"Cannot perform full text search unless an INVERTED index has been created".
The recall legs are gathered without return_exceptions, so one failing leg
fails the whole search request -- every keyword search landing in the window
returned 500. Measured: 55 failures across 3 rebuilds with drop+create, 0 with
create_index(replace=True). Replacing also collapses the live fragment set
identically (7 index files back to 4 after 25 optimize beats), so nothing the
rebuild existed for is lost. Only indexes on columns that are no longer indexed
at all are still dropped -- nothing queries those.

A rebuild that loses the manifest race is now retried rather than deferred to
the next 12h sweep. Lance marks the conflict Retryable and means it: another
process committed first. Retries are recorded as a deadline on the kind
(10min / 30min / 3h) and picked up by the rebuild loop, not slept through --
the loop walks kinds sequentially, so sleeping would park every later kind
behind the backoff (7 kinds x 3h outlasts the cadence itself). The loop tick is
min(60s, cadence) so a shorter configured interval is not quantised.

Removes the empty-index-dir sweep. cleanup_older_than deletes the files under a
superseded _indices/<uuid>/ but leaves the directory, and everos was removing
those with its own rmdir. No LanceDB contract says an empty index dir is
garbage, so this is being raised upstream instead. Note it is a separate gap
from index *files* not being reclaimed under delete_unverified=False (260MB
retained on a 19k-row soak table) -- solving that still leaves the empty dirs.

Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
The rebuild-bound and lock-wait entries were swallowed into the Removed
section when the husk-sweep entry was inserted above them.

Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
@gloryfromca
gloryfromca force-pushed the fix/stall-class-hardening branch from 4acd9a4 to bef0cea Compare August 6, 2026 06:04
zhanghui and others added 3 commits August 6, 2026 15:46
Restores the empty-index-dir sweep with a safety argument instead of a
self-chosen number. Upstream context, read from lance's cleanup.rs: it unlinks
a superseded index's files but never the directory, and contains no rmdir at
all. That is structural, not an oversight -- lance targets object stores, where
paths are flat keys and an empty directory does not exist. Only a local
filesystem materialises them, where they accumulate as inodes (a soak run
reached 13061 dirs, 98% empty) and slow every directory scan.

Three independent guarantees, in order of strength:

1. rmdir cannot delete data. The kernel refuses it on a non-empty directory,
   so no file can be lost whatever the rest of the logic decides -- and because
   the check *is* the operation, there is no check-then-act window to race.
2. Live indexes are excluded by UUID, read from list_indices().
3. Anything else must outlive UNVERIFIED_THRESHOLD_DAYS = 7, which is lance's
   own bound for deciding an unreferenced index UUID is dead rather than an
   index build in progress. Matching it means the sweep can never be more
   aggressive than lance itself; the previous 300s was our invention, and that
   is what made it indefensible.

Each guarantee is pinned by the same test and mutation-verified: dropping the
live-UUID check, zeroing the age gate, and swapping rmdir for a recursive
delete each turn it red.

Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
The four cadences were already constructor arguments on CascadeWorker, but
CascadeConfig did not carry them and none of the three production construction
paths passed a config, so the module defaults were unreachable from outside the
code. That is why no soak run shorter than half a day could exercise the 12h
rebuild sweep: not a missing parameter, a config layer that dropped it.

Adds CascadeSettings ([cascade] in default.toml) and CascadeConfig.from_settings,
which the orchestrator now uses when no config is passed -- so the CLI, backfill
and server paths all pick settings up at once.

Deliberately not exposed: the read / write / prune / rebuild deadlines. Those
are hang-catchers sized from measured durations, and both directions are worse
-- too low manufactures failures on a healthy table, too high leaves a wedged
one invisible for longer. Cadences depend on write volume and are a real tuning
axis; deadlines are not. A test pins the exposed field set so a later change has
to state its intent.

Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
agent_case was the one business kind with no handler test, and the storage
soak never writes it either -- four of the seven tables stay at zero rows
there -- so its md -> row contract was unexercised from both directions.

Covers what makes this kind different from its daily-log siblings: it lives
on the agent track, and it embeds task_intent only while approach is
BM25-indexed but deliberately never sent to the embedder. Plus the branches
every handler shares: soft-dependency embedding (no provider -> vector=None,
row still written for keyword-only deployments), optional KeyInsight, the
content_sha256 short-circuit that stops the 30s scanner re-embedding
untouched files, edit detection, and delete-by-path.

Mutation-verified: routing approach into the embedder, and dropping
section:TaskIntent from content_change_keys, each turn the relevant test red.

Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
@gloryfromca
gloryfromca requested review from Kendrick-Song and cyfyifanchen and removed request for Kendrick-Song August 6, 2026 09:39
Two constants now carry the arithmetic instead of leaving it in a chat log.

_HUSK_MIN_AGE_SECONDS states what the 7-day gate costs: nothing reclaims an
empty index dir before then, each is an inode plus a 4KB block, and at ceiling
load that is ~890k dirs / ~3.6GB / 14% of a default 98GB ext4's inodes at the
7-day steady state. Also that this is the worst case and needs sustained
saturation -- a single-user deployment sits four orders of magnitude below it --
and that only ext4 has a fixed inode budget (APFS and xfs allocate
dynamically, Windows is out of scope).

DEFAULT_OPTIMIZE_MIN_INTERVAL_SECONDS gets two things it never said. First, it
is not a visibility delay: a row is searchable as soon as its upsert commits,
because LanceDB flat-scans the unindexed tail -- verified to cover BM25, not
just vector and scalar, which was the leg worth doubting given a missing FTS
index hard-fails rather than degrading. Sparse writes do not wait at all, since
the scheduler uses max(0, interval - elapsed). Second, it is the ceiling on
index-directory growth: past roughly one write per table per interval the beats
coalesce, so the accrual rate is capped by this interval rather than by write
volume, and raising it lowers the cost proportionally. That makes it the knob
to reach for if the empty dirs ever bite -- not the husk threshold.

Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
zhanghui and others added 4 commits August 6, 2026 19:44
The supervisor's restart budget was spent per process lifetime: three
strikes ever, regardless of how long the loop ran healthily between
them. A loop hitting one recoverable transient every few days — each
cleared by a single restart — would still pool those strikes and
SIGTERM a healthy server weeks in, on the 4th, which punishes exactly
the case supervision exists to absorb.

The budget now counts consecutive quick crashes: a body that ran at
least 60s before raising starts a fresh incident with the full ladder.
A deterministic crash-on-entry still exhausts the budget in ~65s. Same
windowed counting as systemd StartLimitIntervalSec / Erlang
max_restarts-per-max_seconds.

Also corrects the husk accrual numbers in the optimize-cooldown
docstring to the ~14-day effective reclaim horizon (see the sibling
lancedb commit for why the age gate doubles).

Mutation-verified: with the reset removed, the new test exits after
run 3 instead of surviving to run 5.

Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
By the time the sweep runs, the cleanup commit — the thing prune exists
for — has already succeeded, and the sweep is best-effort by contract.
Letting its deadline escape prune() billed the failure to the wrong
account: the optimize scheduler counted a prune failure (feeding the
fallback-rebuild threshold) and the prune-staleness clock stopped
advancing, so both alarms reported a cleanup stall that did not happen.
Same defect shape as the alert counter the fallback rebuild used to
zero: an auxiliary path corrupting the main signal's ledger.

Reachable, not theoretical: sweep time is proportional to dir count
(~35us/dir measured) and the ceiling-load steady state sits right at
the 60s budget. The timeout is tolerable exactly because it is now
swallowed — and the orphaned worker thread finishes the walk anyway, so
the reclamation still happens.

Also corrects the age-gate docstrings: the gate reads st_mtime, which
POSIX bumps when lance's cleanup empties the husk, so the effective
reclaim horizon is file wait + 7 days (~14 days total) and the
ceiling-load steady state is ~1.8M dirs / ~7GB, twice the previously
recorded figure. The "never more aggressive than lance" property is
unaffected (it is strictly more conservative).

Mutation-verified: with the try/except removed, the new test fails on
the escaping VectorStoreBusyError.

Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
300s sat at the edge of what the docstring itself calls a legitimate
hold (a large migration is minutes of O(rows) work), so the worst
honest migration turned every waiting process's startup into a
LockError crash. Now 1800s: the wait has been visible since the first
poll (memory_root_lock_waiting), and against the one case the bound
exists for — a holder alive but wedged — giving up at 5 minutes buys
nothing over 30, because the timeout's job is diagnosis, not recovery.

The timeout message now says which way to look: the kernel releases a
dead holder's flock automatically, so reaching the timeout means the
holder is alive — inspect that process instead of retrying this one.

Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
Supervisor bullet gains the per-incident budget, the sweep bullet gains
the ~14-day effective horizon and the swallowed timeout, and the lock
bullet records the 30min default with its sizing rationale.

Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
zhanghui and others added 3 commits August 6, 2026 20:15
The sibling test covers one side -- a deadline miss must not bill prune's
ledger. Nothing covered the other: widening the catch to `except Exception`
passes every other test in the file, and would turn a genuine fault in
_remove_empty_index_dirs (a TypeError after a signature change, a permission
error on the index dir) into a silent removed = 0 with no signal anywhere.
That is the failure shape this module keeps being audited for, so the
narrowness of the catch needs its own guard.

Found by mutating the catch rather than by reading it.

Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
The two maintenance jobs park on each other -- whichever arrives second waits
on the first -- so the two waits are one hazard seen from opposite ends. The
rebuild side was bounded; this side was left open on the argument that
rebuild_indexes carries its own 300s deadline. That deadline covers its
critical section, not the task's dispatch and teardown around it, so the
transitive bound was never real.

While the runner waits, its per-kind task slot stays occupied, every
_schedule_optimize call short-circuits on it, and that table silently stops
being pruned -- the same shape as the stall this branch has been chasing.

Bounded at 180s. On expiry the beat is skipped rather than run: compacting
under a live rebuild is the interleaving the wait exists to prevent, and both
commit on the same manifest. Writes keep the dirty flag set, so the next beat
retries.

Mutation-verified: replacing the timeout with a plain await hangs the new test
until its own guard fires.

Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
@gloryfromca
gloryfromca merged commit 8024fe5 into main Aug 7, 2026
9 checks passed
@gloryfromca
gloryfromca deleted the fix/stall-class-hardening branch August 7, 2026 03:12
Kendrick-Song added a commit that referenced this pull request Aug 7, 2026
#392 landed on main with its entries under [Unreleased] and no version
bump. Since 1.2.3 ships that code, leaving them there would have the
release notes disclaim work the release contains. Merged section by
section into [1.2.3] and dated it to the actual release day.
gloryfromca pushed a commit that referenced this pull request Aug 7, 2026
…#393)

* feat(ome): exponential backoff + jitter between retry attempts

Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>

* feat(events): carry case body + vector on agent skill chain

* feat(strategies): populate extended agent-skill chain events

* feat(md): AgentSkillReader.list_by_cluster for md-first skill enum

* fix(strategies): rescue extract_agent_skill from cascade-lag dead-letter

Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>

* fix(agentic): honor radius, use kind-shaped rerank, non-empty passage

Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>

* feat(api/ome): expose dispatched + runs, distinguish not_dispatched

Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>

* chore(release): v1.2.3 — agent-skill rescue + OME/agentic contracts

* fix(agentic): drop inert radius plumbing; correct release docs

* fix(md): sanitize LLM-generated skill names against path traversal

AgentSkillFrontmatter.name comes straight from LLM output
(memory.strategies.extract_agent_skill) and was concatenated
unsanitized into the skills/skill_<name>/ directory segment on both
the write path (agent_skill_writer._skill_dir) and the read path
(agent_skill_reader._skill_dir). Given a sufficiently long ../ prefix,
the write target could escape the memory root (CWE-22). A live run
also produced a skill name containing spaces and CJK characters,
proving the "keep snake_case" docstring convention on
AgentSkillFrontmatter.name is not enforced at runtime.

This is the same class of defect already fixed for knowledge-upload
titles/categories. Promote that fix's sanitizer
(knowledge_writer._sanitize_dirname) to a shared primitive,
everos.core.persistence.markdown.sanitize_dirname, so there is one
CWE-22 defense for md directory names instead of two independently
maintained copies:

- New core/persistence/markdown/path_safety.py holds sanitize_dirname
  (idempotent: sanitize(sanitize(x)) == sanitize(x)), exported through
  the markdown + persistence facades.
- SkillPathMixin gains skill_dir_name(), the single sanitization point
  both AgentSkillWriter._skill_dir and AgentSkillReader._skill_dir now
  derive from, replacing their previous independent string
  concatenation.
- KnowledgeWriter now imports the shared sanitize_dirname instead of
  keeping its own private copy.
- AgentSkillFrontmatter.name gains a field_validator rejecting path
  separators / ".." as defence in depth, so a hand-edited SKILL.md is
  caught on parse rather than silently relocating the skill on the
  next write.

Idempotency is what keeps the reader and writer in agreement even
though they recover a skill_name from different sources:
list_by_cluster derives it from the on-disk (already-sanitized)
directory name, while extract_agent_skill._hydrate_algo_skills
re-reads using the frontmatter's raw name field. A regression test
(test_agent_skill_reader.py) seeds a skill whose frontmatter name
contains CJK + a space and asserts both routes resolve to the same
file.

No data migration: agent-skill extraction has never once succeeded
before this branch (the cascade-lag defect this branch fixes meant
.skills/ was never created), so there is no legacy skill corpus whose
directory names would change under the new sanitizer.

Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>

* test(e2e): make the agent-skill chain assertion real

tests/conftest.py's autouse fixture pins embedding + rerank capability
to unavailable for hermeticity, and this test never opted back in.
trigger_skill_clustering and extract_agent_skill both body-guard on
get_embedding_capability().available and return early, so the module
docstring's "real embedder" claim was false and the skill chain never
ran: measured log counts were skill_cluster_updated=0,
agent_skills_extracted=0, strategy_gated_off_embedding_unavailable=10.
The three skill assertions were assert len(...) >= 0 — always true —
with a comment blaming "LLM-dependent" flakiness for a count that was
in fact deterministically zero. This is why a defect that made
agent-skill extraction fail 4/4 in production reached a release: there
was no working e2e coverage of the chain.

- New _opt_in_real_embedding_and_rerank autouse fixture, scoped to this
  file only, resets everos.component.embedding.accessor._capability and
  everos.component.rerank.accessor._capability to None (the mechanism
  the global fixture's own docstring prescribes) so both capabilities
  rebuild from the real .env credentials tests/e2e/conftest.py already
  loads. Restores to None on teardown; every other test keeps its
  hermetic default.
- Replaced the three vacuous per-agent assertions with one aggregate
  floor across all three agents (>= 1 total skill). A per-agent floor
  would be flaky: extract_agent_skill has no cluster-size gate, only
  everalgo's per-case skip_quality_threshold, so a single low-quality
  trajectory can legitimately yield 0 skills for one agent.
- Added a sharper, defect-specific check: assert no dead-lettered
  extract_agent_skill run in OME's run_record (via
  OfflineEngine.list_runs), since a dead-letter (retries exhausted)
  is unambiguously a failure, unlike a quality-gated 0-skill outcome.
- Corrected the module docstring's "real embedder" claim and the old
  "# 4.5" comment's reasoning: extract_agent_skill has no cluster-size
  gate, only everalgo's per-case quality threshold.

Unexecuted: this test is slow + live_llm and this machine has no
provider credentials (the verification .env was deleted), so make ci
does not run it and it could not be run here. Verified by inspection
instead: ran the test file with -m "" to override the marker
deselection and confirmed it proceeds past the new fixture and
through app lifespan startup without error, failing only at the
expected point — LLMNotConfiguredError from the missing API key —
which confirms the fixture and imports are wired correctly and the
only blocker is the missing credentials, not a bug in this change.

Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>

* fix(strategies): sanitize skill name before frontmatter construction

Follow-up to afe1609 (path-traversal sanitization). That commit added a
field_validator on AgentSkillFrontmatter.name rejecting path separators
or "..", intended as a read-side defence for hand-edited SKILL.md
files. But _persist_skill (memory/strategies/extract_agent_skill.py)
constructs AgentSkillFrontmatter(name=skill.name) with skill.name
straight from LLM output — the raw, unsanitized string — so the
validator actually fires on the write path too. Sanitization already
makes the on-disk path safe (SkillPathMixin.skill_dir_name), so an
LLM emitting a traversal-shaped name (reachable via prompt injection,
since the LLM's input is user conversation content) gained nothing
from the validator except a new failure mode: ValidationError ->
strategy raises -> OME retries with backoff -> dead-letter -> that
case's skill is permanently lost. A DoS vector introduced by a
security fix, and it also contradicted the validator's own docstring
("catches a hand-edited SKILL.md").

Also fixes a latent second bug in the validator itself, caught by the
new tests below: it rejected any name containing the substring "..",
but sanitize_dirname keeps "." as a safe character, so
"../" * 8 + "tmp/pwned" sanitizes to "................tmppwned" —
still containing ".." many times over. The validator would have
rejected the sanitizer's own safe output. Narrowed the check to actual
path separators or the name being exactly ".." (the only case where
".." functions as a real traversal component when there's no separator
left to combine it with).

Fix:

- SkillPathMixin gains sanitize_skill_name(skill_name) — the bare
  sanitized name (no skill_ prefix), factored out of skill_dir_name so
  both share one sanitizer call.
- _persist_skill now sanitizes skill.name via sanitize_skill_name
  once, up front, and uses that same sanitized string for
  AgentSkillFrontmatter.id, .name, and the writer.write_main() call.
  A traversal-shaped LLM name is now made filesystem-safe before it
  ever reaches the frontmatter constructor, instead of tripping the
  validator.
- The validator's docstring now describes actual behaviour: the write
  path pre-sanitizes, so the validator only fires for a name that
  bypassed the writer (e.g. a hand-edited file, or any other direct
  AgentSkillFrontmatter construction that skips pre-sanitization).

Bonus: with the write path pre-sanitizing, frontmatter.name becomes
byte-identical to the directory-derived name for LLM-written skills —
an identity, not merely an idempotency argument. This also closes the
gap in the previous commit's reader/writer test, which proved
idempotency generically but never drove an adversarial name through
the actual production write path end-to-end.

Tests:
- test_agent_skill.py: constructing AgentSkillFrontmatter with a
  pre-sanitized adversarial name (mirroring _persist_skill's own call
  shape) succeeds and yields a separator-free name; the read-side
  rejection test for bypassed/hand-edited names is unchanged and still
  passes with the narrowed check.
- test_agent_skill_writer.py: new parametrized identity test — for
  both an adversarial and a CJK/space raw name, sanitize once, write
  via that sanitized name, and assert frontmatter.name equals the
  directory-derived name exactly.
- test_agent_skill_reader.py: docstring updated to clarify its
  existing round-trip test now covers the bypass case (a caller that
  writes via a raw, unsanitized name directly through the writer,
  skipping _persist_skill's pre-sanitization) rather than the normal
  production path, which is proven as an identity by the writer test
  above.
- Existing test_extract_agent_skill.py strategy tests (snake_case
  fixture names) are unaffected — sanitize_dirname is the identity
  function for already-safe names.

Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>

* fix(md): reject degenerate sanitizer results, read globbed paths

Security review of 0c6820f found it did not close the DoS it was meant
to close: sanitize_dirname("../") returns ".." verbatim, because "."
is a safe character and is not stripped by the character-class filter
— only the leading "/" is removed. sanitize_skill_name("../") ->
sanitize_dirname("../") -> "..", and AgentSkillFrontmatter(name="..")
still raises ValidationError (name == ".." is exactly the case the
narrowed validator rejects). Same dead-letter DoS as 0c6820f, just a
shorter payload; the previous commit's tests only exercised the long
"../" * 8 + "tmp/pwned" payload, which happens to sanitize past the
fixpoint. The same fixpoint is a real one-level directory escape on
the knowledge path, which has no skill_ prefix to protect it:
Path(root) / sanitize_dirname("../", "Others") / "doc_123" resolved to
root/doc_123, skipping the category directory entirely.

Fix (path_safety.py): sanitize_dirname now falls back on "", ".", or
".." instead of only "". This one change closes both the skill
dead-letter DoS and the knowledge one-level escape, since both callers
already route through this single primitive. Also NFC-normalizes the
input before the character filter (unicodedata.normalize("NFC", raw)),
so an NFD-decomposed accented character (base letter + combining
mark, which is not \w) no longer silently loses its accent. Rewrote
the docstring, which previously claimed "..  sequences are always
stripped" (false — "." is explicitly a safe character) and "cannot
escape the directory it is concatenated into" (false for an unprefixed
caller before this fix); it now states what actually holds: no
separator survives, so the result is always exactly one path
component, and it is never "", ".", or "..".

Also fixes (per review, cheap and worth doing alongside):

- AgentSkillReader.list_by_cluster previously globbed skill_*/SKILL.md,
  stripped the prefix to recover a name, then called read_main(name),
  which re-derives (and re-sanitizes) the path from that name. Any
  on-disk directory whose suffix was not already a sanitizer fixpoint
  (e.g. "skill_My Skill", a raw space) re-derived to a path that
  doesn't exist and was silently dropped. Since list_by_cluster is the
  documented strong-consistency existence check, a dropped skill would
  make the LLM emit add() for a skill that already exists, duplicating
  it at the sanitized path and orphaning the original. Fixed by having
  list_by_cluster read each globbed path directly (new _read_path
  helper, shared with read_main) instead of round-tripping through a
  recovered name — the reader never derives a path at all on this
  route, which is a stronger guarantee than the idempotency argument
  the docstrings previously leaned on.
- e2e test: made fixture ordering explicit — the embedding opt-in
  fixture now takes _reset_embedding_capability_singleton and
  _reset_rerank_capability_singleton as parameters so pytest's
  dependency graph guarantees correct ordering, rather than relying on
  collection order between conftest files. Added a positive
  "extract_agent_skill actually ran" assertion (any status) before the
  dead-letter check — without it, the dead-letter assertion alone is
  vacuously satisfied by a strategy that never executed at all; it was
  only meaningful before because the skill-count floor happened to run
  first. Dropped the rerank capability opt-in and the module
  docstring's "real reranker credentials" claim: nothing on the
  agent-skill write path touches rerank, so opting it in only widened
  the credential surface with no coverage benefit.
- CHANGELOG: corrected the validator description (rejects a path
  separator or being exactly "..", not any string containing ".."),
  and added the previously-missing user-visible fact that
  AgentSkillFrontmatter.name and the agent_skill LanceDB primary key
  now hold the sanitized name, not the raw LLM output.

Tests: parametrized the sanitize -> construct -> (write, for the
writer-level test) tests over a boundary family instead of one long
payload: "..", "../", "/../", ".", "./", "!!!" (empty), "a" * 200
(truncation), a CJK+space name, and the original "../" * 8 +
"tmp/pwned". Each case asserts the sanitized name is a single
component, is never "" / "." / "..", frontmatter construction
succeeds, and (writer-level) frontmatter.name is byte-identical to the
directory-derived suffix. New test_path_safety.py cases pin the
degenerate-fixpoint fallback directly, the knowledge-style unprefixed
one-level-escape repro, and NFC normalization. New
test_list_by_cluster_finds_skill_whose_directory_suffix_has_a_space
reproduces the exact list_by_cluster drop bug against a directory
written outside the writer entirely.

Explicitly not in scope (per review): the collision behaviour where
"fix django" and "fix_django" now map to the same directory is a real
product-decision question the reviewer is raising separately, not
touched here.

Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>

* docs(md): record the skill-name collision trade-off

No behaviour change. Documents a product decision the coordinator made
explicit: sanitize_dirname is lossy, so distinct raw skill names can
collapse onto the same directory ("fix django" and "fix_django" both
become "fix_django"; "fix!django" and "fixdjango" both become
"fixdjango"; names differing only past the 50-char cap also collide).
Because AgentSkillWriter.write_main is a full-file replace and the
LanceDB primary key is f"{agent_id}_{sanitized_name}", a collision
means the later skill silently overwrites the earlier one, losing its
accumulated source_case_ids, maturity_score, and body.

This is accepted rather than mitigated: the LLM's add/update decision
for a skill is keyed on the name it sees, so a collision usually reads
as an intended update anyway; and adding a disambiguating suffix would
break the frontmatter.name == directory-suffix identity the
reader/writer seam (from 0c6820f) relies on.

- SkillPathMixin.sanitize_skill_name docstring now states the
  collision consequence and the two reasons it is accepted, so a
  reader does not have to derive them.
- sanitize_dirname's docstring gains one line: the function is lossy
  and not injective; callers that need distinct outputs for distinct
  inputs must disambiguate themselves. General primitive — the
  knowledge path calls it too.
- CHANGELOG: added the collision consequence to the existing
  path-traversal entry, next to the already-documented fact that name
  / the LanceDB key hold the sanitized value.

Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>

* fix(md): return skill bodies from list_by_cluster; correct docs

Security review of 1b8cf11 + add842d found the list_by_cluster fix was
incomplete: it stopped its own enumeration from dropping a skill whose
directory suffix wasn't a sanitizer fixpoint, but the caller
(_hydrate_algo_skills) still re-read each selected skill by
fm.name via read_main, which re-derives (and re-sanitizes) a path from
that name and drops it there instead. Reproduced on a real
filesystem: skill_My Skill/ enumerates fine, but
read_main("My Skill") re-derives to skill_My_Skill/ and misses. The
drop moved one layer downstream; existing_relevant_skills was empty
before and after the prior fix.

Fix: list_by_cluster now returns (frontmatter, body) pairs instead of
frontmatter alone, so the caller never needs a second, name-based
read. _select_existing_skills / _rank_skills_by_relevance updated to
carry (fm, body) tuples through selection; _hydrate_algo_skills is
deleted — the body is already in hand, so there's nothing left for it
to do. This closes the drop for real, removes the second disk read
(the 2n-read concern carried since Task 4), and makes "the reader
never derives a path" true end-to-end rather than true only for
list_by_cluster's own enumeration step.

New end-to-end regression test
(test_select_existing_skills... / test_existing_skills_reaches_llm_for_skill_whose_directory_has_a_space)
seeds a skill_My Skill/ directory directly on disk (bypassing the
writer) and runs the real extract_agent_skill strategy against it,
asserting the skill reaches existing_relevant_skills with non-empty
content — the property the previous commit's test docstring claimed
but the code didn't yet deliver. The reader-level regression test
gained the same body assertion.

Also, per review:

- path_safety.py: corrected the NFC docstring claim, which was wrong
  for the ~1,082 Unicode composition-exclusion codepoints (e.g.
  Devanagari क़/ख़, U+0958/U+0959) — NFC decomposes an
  already-precomposed exclusion character instead of preserving it, so
  the combining mark is stripped either way. Scoped the claim to
  "best-effort for the common case", not a guarantee for every script.
  New test pins this directly.
- Dropped the e2e test's unused _reset_rerank_capability_singleton
  fixture parameter: the reviewer adjudicated the earlier instruction
  conflict the other way — ordering is only meaningful between
  fixtures that touch the same state, and this fixture never reads or
  writes the rerank capability at all.
- Widened the skill-name collision documentation (SkillPathMixin.sanitize_skill_name,
  CHANGELOG) beyond dropped-punctuation / space-collapse / truncation
  to the larger case: every combining mark is non-\w and is stripped
  regardless of script, so e.g. Devanagari "किताब" and "कताब" both
  collapse to "कतब" (same for Thai tone marks, Hebrew niqqud, Arabic
  harakat).
- Corrected the collision justification: because _persist_skill
  sanitizes before frontmatter construction, the LLM sees the
  already-sanitized name in existing_relevant_skills, so a colliding
  raw name is an *affirmative* decision that two skills are different,
  not a probable intended update. The decision to accept collisions
  still stands, but on its real grounds: a disambiguating suffix would
  break the fm.name == directory-suffix identity the reader/writer
  seam relies on, and detecting-and-raising would reintroduce the
  dead-letter DoS.
- Merged two consecutive "# -- Internals --" banners in
  agent_skill_reader.py into one.

Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>

* fix(md): skip unparseable SKILL.md instead of failing the cluster

`list_by_cluster` only handled a missing file, so a ValidationError from
`_read_path` aborted the whole enumeration. That enumeration is what
feeds `extract_agent_skill` its existing skills, so one bad SKILL.md
starved every skill in the cluster and dead-lettered that cluster's
extraction on every subsequent run -- the permanent-failure mode this
md-first read path was introduced to eliminate. The write path already
pre-sanitizes to avoid exactly this; the read path was left open.

The trigger surface is the whole schema, not just the traversal
validator this PR added: `_read_path` validates the full
`AgentSkillFrontmatter`, so a field a later revision makes required
would take out every existing file at once. Reproduced both ways.

`read_main` still propagates -- a caller naming one specific skill needs
an error, since `None` already means "not created yet" and reusing it
for "exists but is corrupt" would let an upsert overwrite the damage.

Also moves this route's `OfflineEngine` import under TYPE_CHECKING. It
is used only to annotate `_summarize_runs`, and an eager import
contradicted the deferred `_get_engine` import a few lines below. Note
this saves nothing at startup today: `service.memorize` imports the
engine eagerly to construct it, so any app process pays the ~750ms
apscheduler cost regardless.

* docs(md): correct two docstrings, add the case-collision dimension

Three fixes to claims that did not match behavior:

- `_rank_skills_by_relevance` claimed no skill is silently dropped from
  the prompt. The backfill loop is capped at MAX_SKILLS_IN_PROMPT, and
  the function only runs when the cluster already exceeds that budget, so
  skills beyond K are dropped by design. Reworded to what the backfill
  actually guarantees: a lagging index cannot under-fill the prompt.

- `sanitize_skill_name` enumerated collision causes in detail but omitted
  case, the dimension an LLM varies most freely. "Fix Django" and "fix
  django" sanitize to two distinct names -- two LanceDB rows, but one
  directory on a case-insensitive filesystem (macOS APFS, Windows NTFS
  defaults), so the index advertises a name whose content was overwritten.

- The same docstring justified accepting collisions partly on a
  disambiguating suffix breaking the `frontmatter.name` = directory-suffix
  identity. It would not: writing "fix_django_2" into both keeps that
  intact. Replaced with the real reason it is deferred rather than
  dismissed -- it needs a collision probe and a case-folding rule.

Adds the knowledge-writer sanitization tests that were missing entirely:
swapping in the shared primitive changed NFD input ("Résumé" no longer
degrades to "Resume") and made a "." / ".." topic fall back. Knowledge
upload predates this PR, so unlike skills it has a corpus whose
directory names those first cases affect. Both tests verified red against
the 1.2.2 sanitizer.

* docs(changelog): scope the migration claim, record run_record growth

Three corrections to the 1.2.3 entry:

- "No data migration" was asserted for the whole sanitization change but
  only holds for agent skills, which have no corpus because extraction
  never succeeded. Knowledge upload predates this release and does have
  one: NFD topics and `.`/`..` topics resolve to a different directory
  now. Scoped the claim and spelled out both cases.

- Added the case dimension to the collision list, and replaced the
  "disambiguating suffix breaks the name = directory identity" reason
  with the accurate one -- it does not break it, it just needs a probe
  and a case-folding rule, so it is deferred rather than rejected.

- Recorded that `SkillClusterUpdated` now persists a 1024-dim vector in
  `run_record.event_payload`: ~0.8 KB to ~14 KB per record, ~14 MB per
  strategy at the default 1000-record ring buffer. Operators sizing
  ome.db need this number, and it was not stated anywhere.

* fix(strategies): ship extract_foresight disabled by default

The sender scan reads `m.role` off every memcell item, but only
ChatMessage carries it: ToolCallRequest has `sender_id` and no `role`,
ToolCallResult has neither. So any memcell holding a tool call raises
AttributeError before the first sender resolves -- correct on plain user
chat, guaranteed to fail on agent trajectories, where it burns its
max_retries budget and dead-letters on output nothing consumes today.

Flipped the decorator rather than `default_ome.toml`, because `everos
init` skips an existing `~/.everos/ome.toml` (init_cmd.py:85), so a
template edit would reach new installs only. The toml opt-in is left
working on purpose -- a chat-only deployment does get correct
foresights -- and documented in both the module docstring and the
template comment.

This is a stop-gap. The fix is per-episode extraction, like
atomic_fact, which needs an everalgo entry point that does not exist
yet.

The one test that used foresight as its UserPipelineStarted subscriber
now opts back in through that same toml key, so the opt-in path is
covered rather than worked around. It has to wait for the override to
reach the registry first: ConfigReloader.start() fires its initial load
as a task, so engine.start() returns before ome.toml is applied, and an
emit inside that window is judged against the coded defaults and
dropped by the enabled gate with no redelivery.

* fix(ome): hold engine_sem per attempt, not across the retry chain

The backoff this PR added slept inside the semaphore block, so a run
waiting to retry kept its concurrency slot. That turns a partial outage
into a total stall: with max_concurrent_runs slots and a 1s/2s/4s
backoff, enough simultaneously-failing runs park every slot in
asyncio.sleep and starve strategies that would have succeeded.

The cap exists to bound concurrent strategy work -- LLM calls,
embeddings, storage IO -- and a sleeping coroutine consumes none of it.
Backpressure on the failing work is intended; backpressure on everything
else is not. Semantics change is deliberate and stated in the docstring:
the cap still applies to execution, no longer to waiting.

The guard uses a single-permit semaphore so locked() is unambiguous, and
asserts a second waiter actually acquires -- locked() alone would pass on
an implementation that freed the slot but left waiters unable to take it.
Verified red against the previous structure.

* fix(strategies): reap the directory a renamed skill leaves behind

everalgo treats a name change as a first-class update: _apply_update
preserves prior.id while swapping the name, so _persist_skill wrote the
skill to a new skill_<new_name>/ and the old directory survived with the
same cluster_id.

That is not a cosmetic leak now. Since existing skills are read from
markdown rather than LanceDB, the orphan returns in the next run's
existing_relevant_skills as a duplicate of a skill the LLM already
renamed -- feeding exactly the add-instead-of-update full-replace clobber
this PR set out to close, once more per rename. Reconciliation keys off
skill.id, the only field that survives a rename (a fresh add mints a
uuid4 and can never match), and never deletes a name another emitted
skill just claimed.

Also in this pass:

- AgentSkillWriter.delete_skill, the one destructive operation here. It
  fails closed: a directory it cannot resolve by the writer's own path
  rule is left alone rather than targeted by anything looser.
- reference_name / script_filename now sanitized on both reader and
  writer. They are appended after the skill_<name> segment, so
  skill_dir_name never covered them. Zero callers in src/ today; closing
  it before progressive disclosure wires them up.
- Agentic case rows with every passage field empty fall back to a
  placeholder instead of raising ValueError in everalgo's _format_docs
  and 500ing a whole search the row merely appears in.
- The retire op is documented as unimplemented rather than left implied.
  aextract returns a flat list with no discriminator, so a retirement
  arrives as an ordinary low-confidence skill and is written back like
  any other. Honouring it means either giving an LLM confidence score
  authority to delete the source of truth, or a retired flag that the
  enumeration, cascade, and search all learn to filter on -- a design
  decision, deferred.
- The embedding body-guard comment no longer claims to protect a local
  embed call; this strategy stopped embedding when the vector moved onto
  the event.

* fix(strategies): stop extract_foresight crashing on tool-call memcells

The sender scan read m.role off every memcell item, but only ChatMessage
carries it: ToolCallRequest has sender_id without it, ToolCallResult has
neither. The first tool call raised AttributeError before any sender was
resolved, so the strategy was correct on plain user chat and
dead-lettered every time on agent trajectories.

everalgo contracts for exactly this input -- user_memory/_render
.chat_messages says "the caller need not pre-filter; an
AgentMemCell-shaped MemCell is acceptable input" -- and every other
user-memory extractor gets that for free by delegating. This strategy was
the one place the filter was hand-rolled, and it was hand-rolled wrong.

It stays disabled by default, but for the correct reason: nothing in
EverOS reads foresights yet, so running it spends one LLM call per sender
per memcell on write-only data. The earlier justification (per-episode
extraction needs an everalgo entry point that does not exist) confused
extraction granularity with the crash; granularity is still open, the
crash was one line. Fixing it is what makes the documented ome.toml
opt-in actually usable.

The guard pins both directions: a pure agent trajectory extracts nothing
and never reaches the LLM, and a mixed memcell extracts for human senders
only -- an implementation that stopped raising but scanned tool-call
sender_id values would invent "agent" as a user.

CHANGELOG also records that the stale-index clobber is fully closed only
for clusters at or below MAX_SKILLS_IN_PROMPT; above it LanceDB orders
the markdown candidates, and the skill a lagging index omits is the one
written most recently.

* docs(changelog): fold the merged cascade work into the 1.2.3 entry

#392 landed on main with its entries under [Unreleased] and no version
bump. Since 1.2.3 ships that code, leaving them there would have the
release notes disclaim work the release contains. Merged section by
section into [1.2.3] and dated it to the actual release day.

---------

Co-authored-by: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
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