* feat(storage): resolve the shared sibling-store identity and layout (#3352)
Linked worktrees of one repository resolve to one store under
GITNEXUS_HOME/stores/<key>, keyed by the canonical git common dir. The
resolver reads the .git entry directly, so hot paths spawn no git. Slot
naming moves to a leaf module so storage-resolver and shared-store do not
import each other.
Co-Authored-By: Claude Opus 5.5 (1M context) <noreply@anthropic.com>
* feat(storage): resolve a shared checkout's graph and existing store slot (#3352)
getStoragePaths reads a flat slot's recorded graphPath only for checkout
slots under the stores directory; other paths keep <storagePath>/lbug with
no I/O. A recorded path outside the store's commit graphs is ignored.
resolveStoragePath falls back to an existing store slot for an
unregistered checkout, so reads never move to an empty slot.
Co-Authored-By: Claude Opus 5.5 (1M context) <noreply@anthropic.com>
* feat(analyze): share one immutable commit graph across clean worktrees (#3352)
A linked worktree writes its own slot in the shared store. A new slot
is seeded with a pointer to the nearest commit graph, so a clean
checkout at an indexed commit takes the up-to-date path and writes no
graph. A checkout with local changes gets a copy-on-write private
graph before its first write. After a successful run, a clean checkout
at HEAD publishes its graph into commits/ under a store lock, or drops
it when that commit graph already exists. Commit graphs are never
written after publish.
Co-Authored-By: Claude Opus 5.5 (1M context) <noreply@anthropic.com>
* feat(analyze): seed a worktree's graph from the nearest index (#3352)
A new shared slot is seeded from the store's commit graph nearest to
HEAD, else from this checkout's or the main checkout's
repository-local index (copied under that index's lock, source left in
place). The run that follows is up to date or incremental instead of a
full build. If a pointed-at shared graph has been removed, analyze
falls back to a full build instead of an incremental update over a
missing baseline.
Co-Authored-By: Claude Opus 5.5 (1M context) <noreply@anthropic.com>
* feat(analyze): keep one parse cache per shared store (#3352)
Linked worktrees read and write the parse cache and durable ParsedFile
store under the store's caches/ directory. Before pruning, a run folds
in the chunk keys recorded by every member slot and commit graph, and
the fold, prune and save run under a store-wide cache lock so one
member never evicts another's live chunks.
Co-Authored-By: Claude Opus 5.5 (1M context) <noreply@anthropic.com>
* feat(clean): remove only what no shared-store member references (#3352)
Deleting a shared checkout slot (clean, clean --all, remove, and the
server delete route) recounts references under the store's publish
lock and deletes commit graphs no member points at, then the store
itself once empty. A graph that cannot be deleted (open on Windows) is
reported and kept for the next pass. clean --gc also drops member slots
whose worktree is gone or no longer resolves to the store.
Co-Authored-By: Claude Opus 5.5 (1M context) <noreply@anthropic.com>
* feat(analyze): let a clone opt in to a shared store with --share-with (#3352)
An independent clone joins a linked worktree's shared store only with
analyze --share-with <repo>, and only when its normalized origin URL
matches that member's (credentials stripped, as #2054 compares). The
registry remembers the choice. --no-share moves an opted-in clone back
to its own .gitnexus and reclaims its old slot; linked worktrees always
share and are pointed at GITNEXUS_SHARED_STORE=off instead.
Co-Authored-By: Claude Opus 5.5 (1M context) <noreply@anthropic.com>
* fix(storage): count a shared checkout's commit graph as its code index (#3352)
A clean shared checkout reads a commit graph and owns no graph file, so
the code-index presence check made status report it unindexed and
registry validation skip it. The check now follows the slot's
validated graphPath.
Co-Authored-By: Claude Opus 5.5 (1M context) <noreply@anthropic.com>
* feat(storage): adopt existing worktree indexes and report shared-store state (#3352)
A shared checkout gets <repo>/.gitnexus/store.json pointing at its store
slot; resolution follows it only when it names that checkout's own slot.
An existing local index seeds the slot and is left in place. status
(text and --json) and doctor report the store, whether the graph is
shared or private, and any leftover local index, which
clean --local-index removes while keeping the pointer. With
GITNEXUS_SHARED_STORE=off a previously shared checkout indexes into its
own .gitnexus again and never writes a commit graph.
Co-Authored-By: Claude Opus 5.5 (1M context) <noreply@anthropic.com>
* feat(mcp): read the graph a shared checkout points at (#3352)
MCP, the HTTP API, group sync, augmentation, and the Claude hook (all
three byte-identical copies) resolve a flat slot's graph through
resolveGraphPath instead of joining 'lbug' onto the storage path, so
checkouts at one commit share one open database. The embeddings writers
(embeddings sync and the server embed job) take a private copy first
and never write an immutable commit graph. The post-analyze settle
probe accepts fresh metadata that points at an existing commit graph.
Co-Authored-By: Claude Opus 5.5 (1M context) <noreply@anthropic.com>
* docs: describe the shared worktree index store (#3352)
Co-Authored-By: Claude Opus 5.5 (1M context) <noreply@anthropic.com>
* refactor(storage): reuse helpers across the shared-store code (#3352)
One graph-clone helper replaces two copy-then-rename blocks; clean and
status reuse formatSlotSize; leaving a store reuses
removeSharedStorePointer; withStoreLock is imported from its own module
instead of a re-export.
Co-Authored-By: Claude Opus 5.5 (1M context) <noreply@anthropic.com>
* fix(storage): address review findings in the shared store (#3352)
- Never publish a graph whose build saw dirty files, and never trust a
local-index seed on the up-to-date path; it may hold reverted edits.
- Record slot pointers and reclaim under the publish lock, and reclaim
right after each publish, so a commit graph is never deleted between
publish and pointer save and superseded graphs don't pile up.
- clean --gc decides membership from the registry, so opted-in clones
and a main checkout without worktrees are not dropped.
- Leaving a store re-registers first, so an up-to-date run cannot leave
the registry pointing at a deleted slot.
- Drop pinned branch summaries when an entry moves into a store slot.
- Keep run.cjs and the AGENTS.md runner path inside the checkout.
- MCP handles follow the slot's current graph, and branch scoping reads
the slot's own metadata.
- Cache resolveGraphPath by metadata file identity; look up opted-in
entries with canonical registry paths.
Co-Authored-By: Claude Opus 5.5 (1M context) <noreply@anthropic.com>
* fix(cli): localize help for the shared-store flags (#3352)
--help renders option text from the i18n catalog, so --share-with,
--no-share, clean --gc and clean --local-index need keys in both
locales, not just index.ts literals.
Co-Authored-By: Claude Opus 5.5 (1M context) <noreply@anthropic.com>
* fix(storage): lock the embed-job graph copy and skip it on forced rebuilds (#3352)
The server embed job copies a shared checkout's graph under the slot's
index lock, so a CLI analyze in another process cannot interleave. A
forced rebuild with no embeddings to carry over drops the pointer
without copying a graph it would discard unread.
Co-Authored-By: Claude Opus 5.5 (1M context) <noreply@anthropic.com>
* docs(agents): bump AGENTS.md version for the shared store notes (#3352)
Co-Authored-By: Claude Opus 5.5 (1M context) <noreply@anthropic.com>
* fix(storage): keep shared-store file reads inside checked paths (#3374)
Address CodeQL js/path-injection and js/file-system-race on
shared-store.ts: every filesystem read rebuilds its path under a fixed
parent with an inline path.relative barrier, the .git probe is one read
(EISDIR marks a directory) instead of stat-then-read, and the graph
pointer cache stats and reads through one file descriptor.
Co-Authored-By: Claude Opus 5.5 (1M context) <noreply@anthropic.com>
* fix(storage): address review feedback on the shared store (#3374)
- Hold the slot index lock for the whole server embedding job, not
just the graph copy.
- --no-share re-registers and deletes the old slot under that slot's
index lock, so a running shared analyze cannot re-register it.
- clean --gc previews without --force, like every other destructive arm.
- status reports a pinned branch index as private.
- Slot names prefix Windows device names that carry an extension.
- A slot or store named ..<name> is a legal direct child.
- Shared-store suites run in the serialized lbug-db vitest project and
clear an inherited GITNEXUS_SHARED_STORE.
- Doc and test accuracy fixes.
Co-Authored-By: Claude Opus 5.5 (1M context) <noreply@anthropic.com>
* test(storage): pin shared-store behavior for worktrees of a bare repository (#3374)
Co-Authored-By: Claude Opus 5.5 (1M context) <noreply@anthropic.com>
* fix(storage): address second review round on the shared store (#3374)
- Reject --no-share in a linked worktree before taking any lock or
indexing anything.
- clean --all and remove also delete each shared checkout's pointer.
- Delete an empty store only while also holding its cache lock, and
re-check emptiness under it.
- A store pointer is trusted only when the slot's own metadata names
this checkout; the editable pointer file just says where to look.
- Device names with an extension are prefixed on Windows only, so POSIX
slot names stay stable.
- Test fixtures use the gitnexus-test- prefix the stale-sidecar sweep
recognizes; help text and the private-graph label are accurate.
Co-Authored-By: Claude Opus 5.5 (1M context) <noreply@anthropic.com>
* fix(storage): address third review round on the shared store (#3374)
- clean --gc never collects a slot whose index lock is held: an analyze
holds it until it registers the checkout, so a seeded but not yet
registered slot is busy, not orphaned.
- Reclaim compares absolute paths, so a relative GITNEXUS_HOME does not
make live commit graphs look unreferenced.
- graphPath is followed only into a published <commit>-<featureKey>
dir, never .publish-* staging (TS and all three hook copies).
- clean --gc fails on an unreadable stores root instead of reporting
nothing to collect.
- --no-share help states it is for opted-in clones.
Co-Authored-By: Claude Opus 5.5 (1M context) <noreply@anthropic.com>
* fix(cli): land the English --no-share help and private-graph label (#3374)
These two strings were meant for e2a9467 and d746675 but were left out
of the commit; the zh-CN side landed.
Co-Authored-By: Claude Opus 5.5 (1M context) <noreply@anthropic.com>
* fix(storage): address fifth review round on the shared store (#3374)
- analyze --no-share leaves the shared store even when routed to a
branch sub-index (gate on sharedStore, not placement.branch)
- clean --gc aborts a store whose member listing is unreadable instead
of treating it as empty, and skips non-directory entries under stores/
- reusing an existing commit graph no longer fails a finished analyze
when the redundant private graph cannot be wiped
- a store pointer holding JSON null, a number, a string, or an array is
treated as invalid
- clean, remove, and DELETE /api/repo hold the checkout slot's index
lock while deleting the slot
- the server analyze launcher waits on the checkout slot the worker
actually writes
- sync the Factory hook copy; isolate hook tests from storage overrides;
use a junction for the Windows worktree alias; the relative
GITNEXUS_HOME test now sets a relative home
Co-Authored-By: Claude Opus 5.5 (1M context) <noreply@anthropic.com>
* fix(storage): address sixth review round on the shared store (#3374)
- clean, remove, and analyze --no-share remove the checkout's store
pointer while still holding the slot's index lock, so an analyze that
takes the lock next cannot have its new pointer deleted
- clean --gc does not follow a symlink under stores/ (lstat)
- removing a store pointer keeps the checkout's .gitnexus directory when
it cannot be listed, instead of treating it as empty
Co-Authored-By: Claude Opus 5.5 (1M context) <noreply@anthropic.com>
* fix(storage): address seventh review round on the shared store (#3374)
- clean --gc aborts when the registry cannot be read instead of treating
every member as orphaned; with no registry file it collects only
members whose checkout directory is gone
- seeding from a repository-local index re-reads its metadata under the
index lock, so the copied graph and the saved metadata match
- clean --gc skips a store another collector removed meanwhile, and
reports "no shared stores" when stores/ holds only stray files
Co-Authored-By: Claude Opus 5.5 (1M context) <noreply@anthropic.com>
* fix(storage): address eighth review round on the shared store (#3374)
- removing a checkout's storage unregisters it and removes its store
pointer before deleting the slot directory, which the file lock
backend uses for its lock file; withCheckoutSlotLock becomes
removeCheckoutStorage, used by remove, clean, and DELETE /api/repo,
and analyze --no-share follows the same order
- the clean --gc preview skips a slot whose index lock is held, matching
what --force would drop
Co-Authored-By: Claude Opus 5.5 (1M context) <noreply@anthropic.com>
* feat(storage): share the index store between clones automatically (#3352)
Clones of one repository now share like linked worktrees. A clone whose
normalized origin URL matches another registered, still-present clone
joins that clone's store, or founds one (keyed on its own path) that the
sibling joins on its next analyze. A lone clone keeps its own .gitnexus.
Graphs stay keyed by commit and feature key, so clones only ever share a
graph built from the same commit with the same settings.
`analyze --no-share` now records a lasting opt-out (`shareOptOut` on the
registry entry, preserved across re-registration); `--share-with` clears
it. The analyze worker reports the storage it wrote over IPC so the
server settles a clone's first shared slot.
A query-time base-plus-overlay graph stays out: LadybugDB reads one
database per query. Instead, private graph copies record whether the
filesystem cloned them copy-on-write (sharing unchanged pages on disk)
or made a full copy, and `status` reports it.
Co-Authored-By: Claude Opus 5.5 (1M context) <noreply@anthropic.com>
* fix(storage): never follow a symlinked checkout .gitnexus (#3374)
A checkout whose `.gitnexus` is a symlink (e.g. `.gitnexus -> ..`) made
the shared-store pointer helpers operate on whatever it pointed at:
findLegacyLocalIndex listed the target as a "legacy index", so
`clean --local-index --force` recursively deleted the checkout's
siblings; writeSharedStorePointer wrote store.json/.gitignore there; and
removeSharedStorePointer deleted store.json there and could rm -r the
target directory.
All four now go through probePointerDir, which lstats `.gitnexus` and
accepts it only when it is a real directory whose realpath is
realpath(checkout)/.gitnexus (mirroring stale-branch-slots.ts). Anything
else is left untouched: no legacy index is reported or removed, and no
pointer is written or removed. removeLegacyLocalIndex re-probes after
sizing, just before its delete loop.
Co-Authored-By: Claude Opus 5.5 (1M context) <noreply@anthropic.com>
* fix(storage): never share a graph from a checkout that hides files (#3374)
Trigger: a sparse checkout, a skip-worktree/assume-unchanged entry, or an
uninitialized submodule leaves `git status` clean, and the run's
indexCoverage.dirtyPaths drops paths with no file hash, so publishSharedGraph
published a graph missing those files as the commit graph. seedSharedSlot
then copied the seed's lastCommit into the new pointer slot, so the next
analyze of a sibling hit the up-to-date fast path without hashing.
Fix: add isWorkingTreePristine (storage/git.ts): the unfiltered
listWorkingTreeDirtyPaths must be empty (null fails closed) and every
gitlink in the index must have a checked-out `.git`. publishSharedGraph
requires it instead of isWorkingTreeDirty. seedSharedSlot keeps the seed's
lastCommit only when the seed is at HEAD and the checkout is pristine, so a
clean sibling still fast-paths onto the shared graph; any other seeded
pointer gets an empty lastCommit, like seedFromLocalIndex, and its next run
hash-diffs, then re-points at the commit graph on publish.
Co-Authored-By: Claude Opus 5.5 (1M context) <noreply@anthropic.com>
* fix(storage): keep graphs with pending embeddings out of the shared store (#3374)
Trigger: an analyze that finished with embeddings still owed (meta carries
embeddingCheckpoint) was published as the commit graph, because the
feature key ignores the checkpoint and publish never checked it. The
published meta kept the checkpoint while the graph could never change. The
next run healed the embeddings privately, found the commit graph already
there, wiped its own healed graph and pointed back at the partial one.
Fix: publishSharedGraph treats a checkpointed graph as not shareable, so it
stays private and no published commit graph carries a checkpoint. When the
target commit graph exists but records a checkpoint, has fewer
stats.embeddings than the private graph, or has unreadable metadata, the
checkout keeps its private graph instead of re-pointing. The commit graph
is left as is because other checkouts may read it. Embeddings sync and the
server embed job already privatize a pointer slot before writing
(ensurePrivateSharedGraph).
Co-Authored-By: Claude Opus 5.5 (1M context) <noreply@anthropic.com>
* fix(storage): rebuild a shared slot whose graph is missing (#3374)
A publish interrupted between moving the checkout's graph into
`.publish-<uuid>` staging and renaming staging onto the commit dir left
slot metadata at HEAD with no graph and no graphPath; the next reclaim
deleted the orphaned staging. The up-to-date fast path never checked that
the graph exists, so every later analyze reported "Already up to date"
over a checkout with no index. A failed restore in publishSharedGraph's
catch had the same outcome, and also deleted the staging dir holding the
only copy of the graph.
- run-analyze: for a shared-store slot, stat the graph the checkout reads
(resolveGraphPath for the flat slot, the branch slot's own lbug
otherwise) before the fast path; if it is missing, force a full
rebuild. An incremental run would diff nothing into a fresh, empty
database. Private .gitnexus indexes are unchanged: they only lose their
graph by hand, and metadata-only fast-path fixtures rely on that path.
- publishSharedGraph: when moving the staged graph back fails and it is
still in staging, keep the staging dir, log its path, and skip this
run's reclaim, which would otherwise delete it. The next analyze finds
no graph and rebuilds.
Co-Authored-By: Claude Opus 5.5 (1M context) <noreply@anthropic.com>
* fix(storage): fail safe on unreadable slot metadata during reclaim (#3374)
Trigger: reclaim counted commit-graph references with loadMeta, which
returns null for a torn or unreadable gitnexus.json as well as for a
missing one. A member whose metadata could not be read therefore
"referenced nothing", and the graph it still used was deleted. Separately,
in `clean --gc` an orphan slot that fs.rm could not delete threw out of
reclaim, aborting the collection of every store after it.
Fix: the reference loop reads slot metadata with a local loadMetaStrict.
Only absent metadata (ENOENT/ENOTDIR, same legacy-mirror fallback as
loadMeta) means no reference; any other read error or a parse failure
throws with the file path, like listDirStrict. Every caller already
treats a reclaim throw as best effort (analyze logs "skipped cleanup",
slot removal ignores it) or surfaces it (clean --gc). A failed orphan
slot delete is now kept: it stays a member, so the graph it names is
kept too, and it is reported in ReclaimResult.keptMembers and by a new
clean --gc line. loadMeta itself is unchanged.
Co-Authored-By: Claude Opus 5.5 (1M context) <noreply@anthropic.com>
* fix(server): unregister under the slot lock and answer 409 on DELETE /api/repo (#3374)
DELETE /api/repo called removeCheckoutStorage(storagePath) with no
unregister callback and no checkout path, swallowed every error, and
unregistered later outside the slot lock. For a shared-store slot this
left the checkout's store.json pointer behind, let an analyze re-register
between the slot removal and the unregister, and reported {deleted} even
when the slot lock could not be taken because an analyze held it.
The handler now calls removeCheckoutStorage(storagePath,
() => unregisterRepo(entry.path), entry.path), matching `gitnexus remove`
and `gitnexus clean`, so the unregister and the pointer removal run under
the slot lock; non-shared storage is still removed, then unregistered.
The later standalone unregister is gone. An IndexLockTimeoutError answers
409 and leaves the entry registered; any other failure propagates to the
handler's 500, also with the entry kept so the delete can be retried,
instead of unregistering over leftover index files.
Co-Authored-By: Claude Opus 5.5 (1M context) <noreply@anthropic.com>
* fix(storage): give concurrent sibling clones one deterministic founder key (#3374)
Trigger: two registered clones of one origin, both still on local storage,
analyzing at the same time each saw no sibling store yet and founded a store
keyed on their own checkout path. registeredStore() then kept each clone in
its own store for good, so they never shared a graph.
Fix: when no sibling store exists, siblingCloneStore keys the new store on
the canonical path that sorts first among this clone and its registered
siblings (case-folded on Windows, like registryPathEquals), so every sibling
computes the same key. An existing sibling store still wins. Clones that
already diverged into two stores are not migrated.
Co-Authored-By: Claude Opus 5.5 (1M context) <noreply@anthropic.com>
* fix(storage): keep subdirectories of a clone out of shared stores (#3374)
Trigger: `analyze --skip-git <clone>/pkg` inside a clone with a registered
sibling of the same origin joined, or founded, a clone store. getRemoteUrl
answers from any subdirectory, so siblingCloneStore saw the enclosing
clone's remote. That broke the shared-store invariant that only tree roots
participate.
Fix: resolveOptedInStore now returns undefined for a path with no `.git`
entry. It uses hasGitDir, which accepts a directory or a linked-worktree
file, the same as resolveSharedStore's readCommonDir gate and run-analyze's
repoHasGit. `--share-with` from such a path throws a clear error.
Co-Authored-By: Claude Opus 5.5 (1M context) <noreply@anthropic.com>
* fix(hooks): prefix Windows device names with an extension in hook slot names (#3374)
Trigger: on Windows, storage-slot.ts sanitizeSlotBasename prefixes a
device-name basename that has an extension (`CON.txt` -> `repository-CON.txt`),
but the hook's copy in registry-query.cjs only matched the bare device name.
With GITNEXUS_STORAGE_ROOT set, a checkout named e.g. `con.txt` got a
different slot from the hook than from the CLI, so the hook could not see its
index.
Fix: mirror the platform branch (extension form on win32, bare form
elsewhere) in all four byte-identical registry-query.cjs copies, and point
their header comments at storage-slot.ts. Add a hook-vs-TS parity test over
device-name basenames on both stubbed platforms, and fix the byte-identity
test title to say four copies.
Co-Authored-By: Claude Opus 5.5 (1M context) <noreply@anthropic.com>
* refactor(storage): tidy the shared-store fix series (#3374)
Explain the keptStaging early return where it is checked, reuse the
exported EmbeddingCheckpoint type in the publish test, and drop
review-step labels from test comments. No behavior change.
Co-Authored-By: Claude Opus 5.5 (1M context) <noreply@anthropic.com>
* fix(storage): address ninth review round on the shared store (#3374)
- removeCheckoutStorage: keep the lock-safe order (unregister and drop the
pointer under the slot lock, delete the slot last), but when the final
rm fails, throw an error that says the checkout was already unregistered,
names the leftover slot, and points at `gitnexus clean --gc --force`.
- clean --gc preview no longer sweeps staging files: acquireIndexLock
takes `sweep: false`, which the dry-run reclaim passes.
- listStoreMetaRoots reports completeness; a store directory that cannot
be listed (other than missing) makes the parse-cache prune retain every
chunk instead of evicting keys other members still use.
- clean.shared.kept says "could not be removed" rather than "still open".
- ARCHITECTURE.md describes the stores/<key>/ layout and store.json
pointer; README lists every GITNEXUS_SHARED_STORE off value and that it
also stops clone sharing.
- Tests: close the direct Ladybug connection in finally; fix a fixture
JSDoc.
Co-Authored-By: Claude Opus 5.5 (1M context) <noreply@anthropic.com>
* test(storage): pin the publish gate for cone and sparse-index checkouts (#3374)
isWorkingTreePristine already rejects every sparse mode, because each one
marks left-out entries skip-worktree and `git ls-files -v` expands a sparse
index. Only no-cone was tested; cover cone and cone with a sparse index too.
Co-Authored-By: Claude Opus 5.5 (1M context) <noreply@anthropic.com>
* docs(storage): name the checks that answer recurring review findings (#3374)
Comment-only. The review bot re-derives findings from the code on every
push, so put the refuting fact next to each flagged line: the pristine
check's hidden-path coverage, sparse checkouts being skip-worktree, the
lock-safe unregister-then-delete order, the hook parity test for device
names, and why the stores/ lstat is not a race guard.
Co-Authored-By: Claude Opus 5.5 (1M context) <noreply@anthropic.com>
---------
Co-authored-by: Gergo Magyar <gergomagyar0@gmail.com>
Co-authored-by: Claude Opus 5.5 (1M context) <noreply@anthropic.com>
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