mirror of
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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>
This commit is contained in:
Gergo Magyar
parent
61a8a26528
commit
11acf84239
11 changed files with 177 additions and 24 deletions
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@ -491,9 +491,22 @@ CLI (analyze.ts) → runFullAnalysis(repoPath, options, callbacks)
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└── meta.json # legacy mirror of gitnexus.json, kept in sync (see MIGRATION.md)
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~/.gitnexus/
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└── registry.json # Global repo registry (MCP discovery)
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├── registry.json # Global repo registry (MCP discovery)
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└── stores/<key>/ # Shared sibling index store (see below)
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├── caches/ # parse cache + durable ParsedFile store
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├── commits/<commit>-<featureKey>/ # one immutable graph per commit + settings
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└── checkouts/<slot>/ # one checkout's metadata, membership, and
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# private graph when it has local edits
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```
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The flat `<repo>/.gitnexus/` layout applies to a standalone repository and
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whenever `GITNEXUS_STORAGE_PATH` / `GITNEXUS_STORAGE_ROOT` is set. A repository
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with linked worktrees, and clones with the same `origin` URL, share one
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`stores/<key>/` automatically (a clone opts out with `analyze --no-share`;
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`GITNEXUS_SHARED_STORE=off` turns sharing off entirely). Each sharing checkout
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keeps only a `.gitnexus/store.json` pointer to its store. Path resolution lives
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in `shared-store.ts`.
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Read-only opens self-heal an interrupted checkpoint: the refusal is
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classified and cleared by one writable open (probe + `CHECKPOINT`) before
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the read-only open is retried — see `sidecar-recovery.ts`
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@ -628,7 +628,7 @@ Most `analyze` knobs are also CLI flags (`--workers`, `--worker-timeout`, `--max
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| `GITNEXUS_FTS_STEMMER` | `porter` | Stemmer used when rebuilding BM25/FTS indexes. Use `none` for CJK-heavy repositories, or a language stemmer such as `german`, `french`, or `spanish` for matching repository comments. Re-run `gitnexus analyze --repair-fts` after changing it. | Keyword search quality is poor for non-English comments or identifiers under English stemming. |
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| `GITNEXUS_STORAGE_PATH` | unset (`<repo>/.gitnexus/`) | Complete external index directory. This preserves the existing configuration semantics and takes precedence over `GITNEXUS_STORAGE_ROOT` when both are set. | You already keep one repository index outside its checkout or need one explicit index location. |
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| `GITNEXUS_STORAGE_ROOT` | unset | Absolute root directory for external indexes. GitNexus creates an isolated `<repo-basename>-<canonical-path-hash>/` slot beneath it for each repository, then registers the resolved slot so `status`, MCP, and `serve` can reopen it later. | You want to manage multiple repository indexes centrally or keep generated data outside source checkouts. |
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| `GITNEXUS_SHARED_STORE` | unset (on) | Set to `off` to stop linked git worktrees from sharing one index store; every checkout then indexes into its own `.gitnexus/`. Sharing is also off whenever `GITNEXUS_STORAGE_PATH` or `GITNEXUS_STORAGE_ROOT` is set. | Disk or memory is not a concern, or you want each worktree's index fully independent. |
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| `GITNEXUS_SHARED_STORE` | unset (on) | Set to `off` (or `0`, `false`, `no`) to turn off shared index stores for both linked git worktrees and sibling clones; every checkout then indexes into its own `.gitnexus/`. Sharing is also off whenever `GITNEXUS_STORAGE_PATH` or `GITNEXUS_STORAGE_ROOT` is set. | Disk or memory is not a concern, or you want each worktree's index fully independent. |
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| `GITNEXUS_CONTENT_RETENTION` | `full` | Source-text retention profile: `full` keeps file and symbol text, `symbol` keeps symbol snippets without full file content, and `none` keeps the structural graph without source body text. | You need to reduce persisted source text while preserving graph structure. |
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| `GITNEXUS_SKIP_FTS` | unset | When exactly `1`, skips FTS extension loading and keyword index creation during analyze. Equivalent to `--skip-fts`; a later analyze without either option restores FTS. | Graph-only consumers with their own retrieval, or short-lived indexes that do not need keyword search. |
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| `GITNEXUS_WAL_CHECKPOINT_THRESHOLD` | `67108864` (64 MiB) | LadybugDB WAL auto-checkpoint threshold in bytes. Equivalent to `--wal-checkpoint-threshold <bytes>`. `-1` keeps LadybugDB's stock threshold (~16 MiB). Larger thresholds reduce checkpoint frequency but increase the WAL size at rotation time — choose a smaller value on disk-constrained environments. | You need a larger or smaller WAL auto-checkpoint threshold for your analyze workload. |
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@ -710,7 +710,7 @@ GitNexus uses a **global registry** so one MCP server can serve multiple indexed
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Each `gitnexus analyze` stores the index in `.gitnexus/` inside the repo by default (portable, gitignored). `GITNEXUS_STORAGE_PATH` selects one complete external index directory and preserves the established configuration behavior. To manage multiple repositories under one external directory, set `GITNEXUS_STORAGE_ROOT`; GitNexus derives an isolated `<repo-basename>-<canonical-path-hash>/` slot beneath it for each repository. If both variables are set, `GITNEXUS_STORAGE_PATH` takes precedence. GitNexus registers the resolved slot in `~/.gitnexus/registry.json`, allowing later `status`, MCP, and `serve` commands to reopen the index without repeating the environment variable. LadybugDB connections are opened lazily on first query and evicted after 5 minutes of inactivity (max 5 concurrent). Read-only tools can omit `repo` when only one repo is indexed, an MCP default is configured, or the GitNexus process cwd is inside a registered path without crossing into an unindexed nested Git checkout. Outside those paths—and for mutating tools with multiple indexed repos and no MCP default—pass `repo` explicitly.
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**Worktrees share one index store.** When a repository has linked worktrees (`git worktree add`), the main checkout and every worktree index into one store at `~/.gitnexus/stores/<repo>/` instead of each keeping a full `.gitnexus/`. Checkouts at the same commit with no local changes read one shared, read-only graph: one copy on disk and one open database in MCP. A checkout with uncommitted changes gets its own graph, copied from the nearest shared graph and updated incrementally rather than rebuilt. Parse caches are shared too. Each worktree keeps a small `.gitnexus/store.json` pointer, and an index it had before sharing is left in place; `gitnexus status` reports it and `gitnexus clean --local-index --force` removes it. `gitnexus clean` in one worktree removes only that worktree's slot and any shared graph no other checkout uses; `gitnexus clean --gc` also drops slots whose worktree was deleted. Independent clones of one repository share too: when another registered clone has the same `origin` URL, `gitnexus analyze` in a clone joins that clone's store (or starts one the other clone joins on its next analyze). A lone clone keeps its own `.gitnexus/`. `gitnexus analyze --share-with <name-or-path>` joins a specific checkout's store after checking the `origin` URLs match, and `--no-share` moves a clone back to its own `.gitnexus/` and keeps it out until `--share-with`. On filesystems with copy-on-write clones (APFS, btrfs, XFS) a checkout's private graph shares its unchanged pages with the shared graph on disk; elsewhere it is a full copy, and `gitnexus status` says which. Queries cannot combine two graphs, because LadybugDB reads one database per query, so a checkout with edits always has a complete graph of its own. Set `GITNEXUS_SHARED_STORE=off` to turn sharing off.
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**Worktrees share one index store.** When a repository has linked worktrees (`git worktree add`), the main checkout and every worktree index into one store at `~/.gitnexus/stores/<repo>/` instead of each keeping a full `.gitnexus/`. Checkouts at the same commit with no local changes read one shared, read-only graph: one copy on disk and one open database in MCP. A checkout with uncommitted changes gets its own graph, copied from the nearest shared graph and updated incrementally rather than rebuilt. Parse caches are shared too. Each worktree keeps a small `.gitnexus/store.json` pointer, and an index it had before sharing is left in place; `gitnexus status` reports it and `gitnexus clean --local-index --force` removes it. `gitnexus clean` in one worktree removes only that worktree's slot and any shared graph no other checkout uses; `gitnexus clean --gc` also drops slots whose worktree was deleted. Independent clones of one repository share too: when another registered clone has the same `origin` URL, `gitnexus analyze` in a clone joins that clone's store (or starts one the other clone joins on its next analyze). A lone clone keeps its own `.gitnexus/`. `gitnexus analyze --share-with <name-or-path>` joins a specific checkout's store after checking the `origin` URLs match, and `--no-share` moves a clone back to its own `.gitnexus/` and keeps it out until `--share-with`. On filesystems with copy-on-write clones (APFS, btrfs, XFS) a checkout's private graph shares its unchanged pages with the shared graph on disk; elsewhere it is a full copy, and `gitnexus status` says which. Queries cannot combine two graphs, because LadybugDB reads one database per query, so a checkout with edits always has a complete graph of its own. Set `GITNEXUS_SHARED_STORE=off` (or `0`, `false`, `no`) to turn sharing off for worktrees and clones alike.
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<details>
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<summary><strong>Architecture diagram</strong></summary>
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@ -71,7 +71,7 @@ export const en = {
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'clean.shared.reclaimed':
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'Shared store: removed {{count}} commit graph(s) no checkout references.',
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'clean.shared.kept':
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'Shared store: kept {{count}} unreferenced commit graph(s) that are still open; run `gitnexus clean --gc` later.',
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'Shared store: kept {{count}} unreferenced commit graph(s) that could not be removed (in use or not writable); run `gitnexus clean --gc` later.',
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'clean.shared.storeRemoved': 'Shared store: removed {{path}} (no checkouts remain).',
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'clean.gc.none': 'No shared stores to collect.',
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'clean.gc.keptMembers':
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@ -67,7 +67,7 @@ export const zhCN = {
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'clean.notFoundHere': '当前目录未找到已索引仓库。',
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'clean.shared.reclaimed': '共享存储：已删除 {{count}} 个不再被任何检出引用的提交图。',
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'clean.shared.kept':
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'共享存储：保留了 {{count}} 个仍处于打开状态的未引用提交图；请稍后运行 `gitnexus clean --gc`。',
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'共享存储：保留了 {{count}} 个无法删除的未引用提交图（正在使用或不可写）；请稍后运行 `gitnexus clean --gc`。',
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'clean.shared.storeRemoved': '共享存储：已删除 {{path}}（没有剩余检出）。',
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'clean.gc.none': '没有可回收的共享存储。',
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'clean.gc.keptMembers':
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@ -4927,12 +4927,14 @@ async function runFullAnalysisInner(
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// run's own meta dir, so a single-branch repo folds in nothing → prune
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// set byte-identical to today. A shared store (#3352) folds in every
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// member checkout and commit graph the same way.
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const keyRoots = writeTarget.sharedStore
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// An unlistable store directory starts the fold incomplete, so the
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// retention branch below keeps other slots' chunks.
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const listing = writeTarget.sharedStore
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? await listStoreMetaRoots(writeTarget.sharedStore)
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: [storagePath];
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: { roots: [storagePath], complete: true };
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const siblingKeys = new Set<string>();
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let complete = true;
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for (const root of keyRoots) {
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let complete = listing.complete;
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for (const root of listing.roots) {
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const folded = await collectBranchCacheKeys(root, metaDir);
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for (const k of folded.keys) siblingKeys.add(k);
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if (!folded.complete) complete = false;
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@ -36,7 +36,7 @@ import {
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saveMeta,
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type RegistryEntry,
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} from '../storage/repo-manager.js';
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import { loadMeta, type RepoMeta } from '../storage/repo-meta.js';
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import { isMissingFilesystemError, loadMeta, type RepoMeta } from '../storage/repo-meta.js';
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import {
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cloneStoreKey,
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commitGraphDir,
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@ -337,17 +337,29 @@ export const ensurePrivateSharedGraph = async (
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/**
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* Every directory in the store whose metadata may record parse-cache keys:
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* each checkout slot (its branch slots are read by the caller's per-root
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* fold) and each commit graph.
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* fold) and each commit graph. `complete` is false when a store directory
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* exists but could not be listed: the caller must then keep every cached
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* chunk instead of pruning to a partial key set. A missing directory just
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* has no members, so the listing stays complete.
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*/
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export const listStoreMetaRoots = async (layout: SharedStoreLayout): Promise<string[]> => {
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export const listStoreMetaRoots = async (
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layout: SharedStoreLayout,
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): Promise<{ roots: string[]; complete: boolean }> => {
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const roots: string[] = [];
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let complete = true;
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for (const dir of [layout.checkoutsDir, layout.commitsDir]) {
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const names = await fs.readdir(dir).catch(() => [] as string[]);
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let names: string[];
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try {
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names = await fs.readdir(dir);
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} catch (err) {
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if (!isMissingFilesystemError(err)) complete = false;
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continue;
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}
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for (const name of names) {
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if (!name.startsWith('.')) roots.push(path.join(dir, name));
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}
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}
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return roots;
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return { roots, complete };
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};
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/**
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@ -152,6 +152,11 @@ export interface AcquireOptions {
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pollMs?: number;
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/** Called once when we start waiting on a live holder. */
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onWaitStart?: (holder: LockRecord) => void;
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/**
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* Sweep orphaned staging files once the lock is held. Default true; pass
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* false for a read-only caller, such as a dry run, that must delete nothing.
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*/
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sweep?: boolean;
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}
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export class IndexLockTimeoutError extends Error {
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@ -907,7 +912,7 @@ export const acquireIndexLock = async (
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}
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// Without ownership, a staging file may belong to an active writer.
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try {
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if (!handle.lockFree) sweepStagingArtifacts(lockDir, opts.log);
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if (!handle.lockFree && opts.sweep !== false) sweepStagingArtifacts(lockDir, opts.log);
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} catch {
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/* best-effort */
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}
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@ -168,7 +168,8 @@ export const reclaimSharedStoreLocked = async (
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// whose lock is free, so the preview matches what --force would do.
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let lock: IndexLockHandle;
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try {
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lock = await acquireIndexLock(slot, { timeoutMs: 1 });
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// A preview deletes nothing, not even the staging files the lock sweeps.
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lock = await acquireIndexLock(slot, { timeoutMs: 1, sweep: !opts.dryRun });
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} catch {
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orphans.delete(slot);
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continue;
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@ -439,7 +440,18 @@ export const removeCheckoutStorage = async (
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requireExclusiveIndexLock(lock, `Cannot acquire the index lock at ${storagePath}.`);
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await unregister();
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if (checkoutPath) await removeSharedStorePointer(checkoutPath);
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await fs.rm(storagePath, { recursive: true, force: true });
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try {
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await fs.rm(storagePath, { recursive: true, force: true });
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} catch (err) {
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// The checkout is already unregistered, so a plain `clean` can no longer
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// find this slot. It is now an orphan member, which `clean --gc` removes.
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const reason = err instanceof Error ? err.message : String(err);
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throw new Error(
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`The checkout was unregistered, but its index storage at ${storagePath} could not be deleted (${reason}). ` +
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'Run `gitnexus clean --gc --force` to remove it.',
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{ cause: err },
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);
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}
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} finally {
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lock.release();
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}
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@ -11,6 +11,7 @@ import { SCHEMA_FINGERPRINT } from '../../src/core/lbug/schema.js';
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import {
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ensurePrivateSharedGraph,
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featureKeyOf,
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listStoreMetaRoots,
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publishSharedGraph,
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seedSharedSlot,
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} from '../../src/core/shared-store-analyze.js';
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@ -182,11 +183,15 @@ describe('shared sibling store analyze (#3352)', () => {
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const graph = getStoragePaths(wtB, undefined, layoutOf(wtB).checkoutSlot).lbugPath;
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const db = new lbug.Database(graph, 0, true, true);
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const conn = new lbug.Connection(db);
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const rows = (await (
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await conn.query('MATCH (f:File) RETURN f.filePath AS p ORDER BY p')
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).getAll()) as { p: string }[];
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await conn.close();
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await db.close();
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let rows: { p: string }[];
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try {
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rows = (await (
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await conn.query('MATCH (f:File) RETURN f.filePath AS p ORDER BY p')
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).getAll()) as { p: string }[];
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} finally {
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await conn.close();
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await db.close();
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}
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expect(rows.map((r) => r.p)).toEqual(['a.ts']);
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}, 180_000);
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@ -584,3 +589,57 @@ describe('up-to-date fast path over a missing shared graph (#3374)', () => {
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expect(existsSync(resolveGraphPath(slot))).toBe(true);
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}, 120_000);
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});
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describe('listStoreMetaRoots', () => {
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let tmp: Awaited<ReturnType<typeof createTempDir>>;
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let layout: SharedStoreLayout;
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beforeEach(async () => {
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tmp = await createTempDir('gitnexus-test-store-roots-');
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const root = path.join(tmp.dbPath, 'store');
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layout = {
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key: 'repo-0000',
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root,
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cachesDir: path.join(root, 'caches'),
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commitsDir: path.join(root, 'commits'),
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checkoutsDir: path.join(root, 'checkouts'),
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checkoutSlot: path.join(root, 'checkouts', 'slot-a'),
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canonicalCheckout: null,
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};
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});
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afterEach(async () => {
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vi.restoreAllMocks();
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await tmp.cleanup();
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});
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it('stays complete when the store directories do not exist yet', async () => {
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expect(await listStoreMetaRoots(layout)).toEqual({ roots: [], complete: true });
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});
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it('lists checkout slots and commit graphs, skipping dot entries', async () => {
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await fs.mkdir(path.join(layout.checkoutsDir, 'slot-a'), { recursive: true });
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await fs.mkdir(path.join(layout.checkoutsDir, '.lock'), { recursive: true });
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await fs.mkdir(path.join(layout.commitsDir, 'abc'), { recursive: true });
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expect(await listStoreMetaRoots(layout)).toEqual({
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roots: [path.join(layout.checkoutsDir, 'slot-a'), path.join(layout.commitsDir, 'abc')],
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complete: true,
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});
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});
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it('reports an incomplete listing when a store directory cannot be read', async () => {
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await fs.mkdir(path.join(layout.commitsDir, 'abc'), { recursive: true });
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await fs.mkdir(layout.checkoutsDir, { recursive: true });
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const realReaddir = fs.readdir;
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vi.spyOn(fs, 'readdir').mockImplementation((async (dir: string) => {
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if (dir === layout.checkoutsDir) {
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throw Object.assign(new Error('permission denied'), { code: 'EACCES' });
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}
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return realReaddir(dir);
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}) as unknown as typeof fs.readdir);
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expect(await listStoreMetaRoots(layout)).toEqual({
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roots: [path.join(layout.commitsDir, 'abc')],
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complete: false,
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});
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});
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});
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@ -3,7 +3,14 @@ import { constants as fsConstants, existsSync, readFileSync } from 'fs';
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import fs from 'fs/promises';
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import path from 'path';
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import { afterAll, afterEach, beforeAll, beforeEach, describe, expect, it, vi } from 'vitest';
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import { getStoragePaths, loadMeta, saveMeta } from '../../src/storage/repo-manager.js';
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import {
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getStoragePaths,
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loadMeta,
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readRegistry,
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registerRepo,
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saveMeta,
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unregisterRepo,
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} from '../../src/storage/repo-manager.js';
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import {
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resolveSharedStore,
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sharedStoreLayout,
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@ -14,6 +21,7 @@ import {
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reclaimAfterSlotRemoval,
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readGraphCloneKind,
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reclaimSharedStore,
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removeCheckoutStorage,
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removeLegacyLocalIndex,
|
||||
removeSharedStorePointer,
|
||||
writeSharedStorePointer,
|
||||
|
|
@ -352,6 +360,48 @@ describe('reclaimSharedStore', () => {
|
|||
expect(existsSync(slot)).toBe(true);
|
||||
});
|
||||
|
||||
it("clean --gc preview leaves an orphan slot's staging files in place", async () => {
|
||||
const slot = await member('gone-000000000000', { repoPath: '/nonexistent/checkout' });
|
||||
const staging = path.join(slot, 'lbug.staging.x');
|
||||
await fs.writeFile(staging, 'partial');
|
||||
const preview = await reclaimSharedStore(layout().root, { gc: true, dryRun: true });
|
||||
expect(preview.droppedMembers).toEqual([slot]);
|
||||
expect(existsSync(staging)).toBe(true);
|
||||
});
|
||||
|
||||
it('names the leftover slot and clean --gc when the final slot deletion fails', async () => {
|
||||
const checkout = path.join(tmpHome.dbPath, 'checkout');
|
||||
await fs.mkdir(checkout);
|
||||
const slot = await member('wt-000000000000', { repoPath: checkout });
|
||||
await registerRepo(
|
||||
checkout,
|
||||
{ repoPath: checkout, storagePath: slot, lastCommit: '', indexedAt: '' },
|
||||
{ storagePath: slot },
|
||||
);
|
||||
const realRm = fs.rm;
|
||||
const rm = vi.spyOn(fs, 'rm').mockImplementation((async (
|
||||
target: string,
|
||||
...rest: unknown[]
|
||||
) => {
|
||||
if (String(target) === slot) throw Object.assign(new Error('busy'), { code: 'EBUSY' });
|
||||
return (realRm as (...a: unknown[]) => Promise<unknown>)(target, ...rest);
|
||||
}) as typeof fs.rm);
|
||||
try {
|
||||
await expect(
|
||||
removeCheckoutStorage(slot, () => unregisterRepo(checkout), checkout),
|
||||
).rejects.toThrow(/was unregistered.*gitnexus clean --gc --force/s);
|
||||
} finally {
|
||||
rm.mockRestore();
|
||||
}
|
||||
expect(await readRegistry()).toEqual([]);
|
||||
expect(existsSync(slot)).toBe(true);
|
||||
|
||||
// The leftover is now an orphan member, which `clean --gc` collects.
|
||||
const result = await reclaimSharedStore(layout().root, { gc: true });
|
||||
expect(result.droppedMembers).toEqual([slot]);
|
||||
expect(existsSync(slot)).toBe(false);
|
||||
});
|
||||
|
||||
it('counts references correctly when GITNEXUS_HOME is relative', async () => {
|
||||
const absoluteHome = process.env.GITNEXUS_HOME as string;
|
||||
process.env.GITNEXUS_HOME = path.relative(process.cwd(), absoluteHome);
|
||||
|
|
|
|||
|
|
@ -1142,7 +1142,7 @@ describe('listWorkingTreeDirtyPaths', () => {
|
|||
// that hides committed content (sparse checkout, index bits, an uninitialized
|
||||
// submodule) must never become the commit graph other checkouts reuse.
|
||||
|
||||
/** A repo with one committed file, `a.ts`. */
|
||||
/** A repo with two committed files, `a.ts` and `lib/b.ts`. */
|
||||
function makeCommittedRepo(): string {
|
||||
const repo = makeIsolatedGitRepo();
|
||||
fs.writeFileSync(path.join(repo, 'a.ts'), 'export const a = 1;');
|
||||
|
|
|
|||
Loading…
Add table
Reference in a new issue