codesift-mcp 0.14.0 → 0.15.0

package/dist/cli/commands-maintenance.js

@@ -0,0 +1,409 @@
+import { execFileSync } from "node:child_process";
+import { getBoolFlag, output, die } from "./args.js";
+/**
+ * Delete orphaned per-repo cache artifacts (embeddings/index/meta/bm25/graph)
+ * whose hash stem is no longer in the registry. These accumulate from
+ * re-indexes (hash changes) and ephemeral/test repos that were indexed then
+ * deleted — each leaves multi-GB embedding files behind. Use --dry-run to
+ * preview. Regenerable: re-indexing recreates anything still needed.
+ */
+async function handlePrune(_args, flags) {
+    const { loadConfig } = await import("../config.js");
+    const { withRegistryLock } = await import("../storage/registry.js");
+    const registryPath = loadConfig().registryPath;
+    await withRegistryLock(registryPath, () => handlePruneLocked(flags, registryPath));
+}
+async function handlePruneLocked(flags, registryPath) {
+    const { readFileSync, readdirSync, statSync, unlinkSync } = await import("node:fs");
+    const { join } = await import("node:path");
+    const { loadConfig } = await import("../config.js");
+    const dataDir = loadConfig().dataDir;
+    const dryRun = getBoolFlag(flags, "dry-run");
+    const pruneGraceMs = 5 * 60 * 1000;
+    // Live index hashes from the registry — everything else is orphaned cache.
+    //
+    // A registry entry counted as live even when its `root` no longer existed, so
+    // artifacts for deleted directories were protected indefinitely. Measured
+    // here: 101 of 119 indexed worktrees pointed at directories that were gone,
+    // holding 5.4 GB of embeddings for code that cannot be read. Task branches are
+    // created and deleted constantly, so this accumulates without bound.
+    //
+    // Entries whose root is missing are de-registered first; their artifacts then
+    // fall out as orphans through the sweep below.
+    const live = new Set();
+    const stale = [];
+    const staleHashes = new Set();
+    let reg;
+    let registryDirty = false;
+    try {
+        reg = JSON.parse(readFileSync(registryPath, "utf-8"));
+    }
+    catch {
+        die("prune: cannot read registry.json — aborting so live data is never deleted.");
+        return;
+    }
+    for (const [name, v] of Object.entries(reg.repos ?? {})) {
+        const ip = v.index_path;
+        const root = v.root;
+        // Only a root that is definitively absent counts. An unreadable path (a
+        // permissions error, an unmounted volume mid-check) throws and is treated
+        // as present — the conservative direction, since the cost of keeping a dead
+        // entry is disk, and the cost of dropping a live one is a re-index.
+        let rootGone = false;
+        if (typeof root === "string" && root.length > 0) {
+            try {
+                statSync(root);
+            }
+            catch (error) {
+                const code = error.code;
+                rootGone = code === "ENOENT" || code === "ENOTDIR";
+            }
+        }
+        if (rootGone) {
+            stale.push({ name, root: root });
+            if (typeof ip === "string") {
+                const stem = /^([0-9a-f]{8,})\./.exec(ip.split("/").pop() ?? "")?.[1];
+                if (stem)
+                    staleHashes.add(stem);
+            }
+            continue; // deliberately NOT added to `live`
+        }
+        // Take the HASH STEM with the same shape the sweep below matches, rather than stripping one
+        // known suffix. `.replace(".index.json", "")` silently no-ops on any other form — so after the
+        // SQLite migration an entry whose `index_path` ends in `.index.db` never reached this set, and
+        // every artifact under that hash looked orphaned. Measured 2026-08-07 on one such entry:
+        // 8.33 GB of LIVE data (a 240,706-symbol index plus 3.9 GB of embeddings) was one `prune` away
+        // from deletion. Deriving the stem the same way in both halves of this command is what makes
+        // them agree by construction instead of by coincidence.
+        if (typeof ip === "string") {
+            const stem = /^([0-9a-f]{8,})\./.exec(ip.split("/").pop() ?? "")?.[1];
+            if (stem)
+                live.add(stem);
+        }
+    }
+    // An index database is LIVE if its own `meta` says it describes a directory that still exists —
+    // whether or not the registry knows about it.
+    //
+    // The registry is not the authority on what exists; it is a lookup table, and it drifts. Measured
+    // 2026-08-07: `local/tgm-survey-platform` had been re-registered onto a worktree that was later
+    // deleted, leaving the MAIN checkout's index — 240,706 symbols, and 8.33 GB once its embeddings
+    // are counted — described by no entry at all. Prune classified every byte of it as orphaned.
+    // Twenty-four hours later three MORE databases had drifted the same way, so this is a rate, not
+    // an incident.
+    //
+    // Asking each database who it is costs one small read per unregistered hash, and removes a whole
+    // class of data loss: a repo still present on disk can no longer be deleted because a JSON file
+    // lost track of it. Re-registering also means the next lookup finds it.
+    const rescued = [];
+    const rescuedNames = new Set();
+    // Databases prune could not classify — kept, but SAID so. Protecting them silently is the
+    // difference between "prune deleted nothing unexpected" and "prune is quietly accumulating
+    // files nobody can account for"; only the second is actionable, and only if it is reported.
+    const indeterminate = [];
+    const protectedNames = new Set();
+    for (const name of readdirSync(dataDir)) {
+        const m = /^([0-9a-f]{8,})\.index\.db$/.exec(name);
+        if (!m?.[1] || live.has(m[1]))
+            continue;
+        let db;
+        try {
+            const { DatabaseSync } = await import("node:sqlite");
+            db = new DatabaseSync(`file:${join(dataDir, name)}?mode=ro`, { open: true });
+            const rows = db.prepare("SELECT key, value FROM meta").all();
+            const meta = Object.fromEntries(rows.map((r) => [r.key, r.value]));
+            const root = meta["root"];
+            const repo = meta["repo"];
+            if (!root || !repo) {
+                live.add(m[1]);
+                continue;
+            }
+            statSync(root); // throws when the tree is gone — then it really is garbage
+            // The live guard above is keyed by hash, while registration replaces an
+            // entry by repository name. Do not let an orphan database repoint a
+            // healthy entry that already owns the same name.
+            const existing = reg.repos?.[repo];
+            if (existing?.root) {
+                let existingGone = false;
+                try {
+                    statSync(existing.root);
+                }
+                catch (error) {
+                    const code = error.code;
+                    existingGone = code === "ENOENT" || code === "ENOTDIR";
+                }
+                if (!existingGone) {
+                    // Same root means this database is an older generation and may be
+                    // swept. A different live root is ambiguous, so preserve both and
+                    // leave registry reconciliation to an explicit operator action.
+                    if (existing.root !== root) {
+                        live.add(m[1]);
+                        protectedNames.add(repo);
+                    }
+                    continue;
+                }
+            }
+            live.add(m[1]);
+            protectedNames.add(repo);
+            if (!dryRun) {
+                // Canonical `.index.json` form: `sqlitePathFor()` derives the `.db` from it, and the
+                // live-set above is built from these strings.
+                reg.repos ??= {};
+                const previous = reg.repos[repo];
+                const replacement = {
+                    name: repo,
+                    root,
+                    index_path: join(dataDir, `${m[1]}.index.json`),
+                };
+                if (typeof previous?.symbol_count === "number" && Number.isFinite(previous.symbol_count)) {
+                    replacement.symbol_count = previous.symbol_count;
+                }
+                if (typeof previous?.file_count === "number" && Number.isFinite(previous.file_count)) {
+                    replacement.file_count = previous.file_count;
+                }
+                if (typeof previous?.updated_at === "number" && Number.isFinite(previous.updated_at)) {
+                    replacement.updated_at = previous.updated_at;
+                }
+                if (typeof previous?.last_git_commit === "string") {
+                    replacement.last_git_commit = previous.last_git_commit;
+                }
+                reg.repos[repo] = replacement;
+                registryDirty = true;
+            }
+            rescued.push(repo);
+            rescuedNames.add(repo);
+        }
+        catch (error) {
+            const code = error.code;
+            // Only definite absence makes the database garbage. Any other I/O or
+            // permission failure is inconclusive, so preserve this hash.
+            if (code !== "ENOENT" && code !== "ENOTDIR") {
+                live.add(m[1]);
+                indeterminate.push(name);
+            }
+        }
+        finally {
+            try {
+                db?.close();
+            }
+            catch { /* already closed */ }
+        }
+    }
+    // Safety: an empty live set would mark every artifact orphaned. Refuse rather
+    // than risk nuking a valid (but momentarily empty-looking) data dir.
+    if (live.size === 0) {
+        die("prune: registry lists 0 repos — aborting (refusing to treat all artifacts as orphans).");
+    }
+    // Commit every registry rescue/removal before deleting derived files. If the
+    // atomic registry write fails, prune exits with all artifacts still intact.
+    if (!dryRun && stale.length > 0) {
+        const staleNames = new Set(stale
+            .filter((entry) => !rescuedNames.has(entry.name) && !protectedNames.has(entry.name))
+            .map((entry) => entry.name));
+        const effectiveRepoCount = Object.keys(reg.repos ?? {})
+            .filter((name) => !staleNames.has(name)).length;
+        if (effectiveRepoCount === 0) {
+            die("prune: every registry entry is stale — aborting before registry or artifacts change.");
+        }
+        for (const s of stale) {
+            if (!rescuedNames.has(s.name) && !protectedNames.has(s.name)) {
+                if (reg.repos && s.name in reg.repos) {
+                    delete reg.repos[s.name];
+                    registryDirty = true;
+                }
+            }
+        }
+    }
+    if (registryDirty) {
+        reg.updated_at = Date.now();
+        const { saveRegistryUnderLock } = await import("../storage/registry.js");
+        await saveRegistryUnderLock(registryPath, reg);
+    }
+    // Suffix list lives with the helpers that build these names, so a new artifact kind
+    // cannot quietly become unreclaimable garbage — see ARTIFACT_SUFFIXES.
+    const { artifactPattern } = await import("../storage/_shared.js");
+    const re = artifactPattern();
+    const registryProtectsHash = (hash) => {
+        try {
+            const fresh = JSON.parse(readFileSync(registryPath, "utf-8"));
+            return Object.values(fresh.repos ?? {}).some((entry) => {
+                const file = entry.index_path?.split("/").pop() ?? "";
+                return /^([0-9a-f]{8,})\./.exec(file)?.[1] === hash;
+            });
+        }
+        catch {
+            // An inconclusive registry read must protect data, not authorize deletion.
+            return true;
+        }
+    };
+    let files = 0, bytes = 0, kept = 0;
+    for (const name of readdirSync(dataDir)) {
+        const m = re.exec(name);
+        if (!m)
+            continue;
+        // A stale entry removed during THIS run gets one full run of retention.
+        // The next prune re-evaluates its database metadata before collecting it.
+        if (live.has(m[1]) || staleHashes.has(m[1])) {
+            kept++;
+            continue;
+        }
+        const full = join(dataDir, name);
+        try {
+            const fileStat = statSync(full);
+            // A fresh artifact may belong to an index operation that has not yet
+            // committed its registry entry. Delay collection for one run and also
+            // re-read registry immediately before every destructive unlink.
+            const ageMs = Date.now() - fileStat.mtimeMs;
+            if (ageMs < pruneGraceMs || registryProtectsHash(m[1])) {
+                kept++;
+                continue;
+            }
+            if (!dryRun)
+                unlinkSync(full);
+            bytes += fileStat.size;
+            files++;
+        }
+        catch { /* skip unreadable/already-gone */ }
+    }
+    // Shared-cache versions have no repository hash prefix, so the artifact
+    // sweep cannot discover superseded formats. Keep the current version and
+    // reclaim only older derived cache files.
+    const { currentSharedCacheFilename } = await import("../storage/shared-embedding-cache.js");
+    const currentShared = currentSharedCacheFilename();
+    const currentVersion = Number(/^shared-embeddings\.v(\d+)\.bin$/.exec(currentShared)?.[1]);
+    for (const name of readdirSync(dataDir)) {
+        const match = /^shared-embeddings\.v(\d+)\.(?:bin|ndjson)$/.exec(name);
+        if (!match?.[1] || name === currentShared || !Number.isFinite(currentVersion) ||
+            Number(match[1]) >= currentVersion)
+            continue;
+        const full = join(dataDir, name);
+        try {
+            const fileStat = statSync(full);
+            const ageMs = Date.now() - fileStat.mtimeMs;
+            if (ageMs < pruneGraceMs)
+                continue;
+            if (!dryRun)
+                unlinkSync(full);
+            bytes += fileStat.size;
+            files++;
+        }
+        catch { /* skip unreadable/already-gone */ }
+    }
+    output({
+        indeterminate_databases: indeterminate.length,
+        indeterminate_examples: indeterminate.slice(0, 5),
+        rescued_repos: rescued.length,
+        rescued_examples: rescued.slice(0, 5),
+        stale_repos: stale.length,
+        stale_examples: stale.slice(0, 5).map((s) => s.name),
+        pruned: !dryRun,
+        dry_run: dryRun,
+        orphan_files: files,
+        freed_gb: +(bytes / 1e9).toFixed(2),
+        kept_live_artifacts: kept,
+        data_dir: dataDir,
+    }, flags);
+}
+function listProcesses() {
+    const raw = execFileSync("ps", ["-axo", "pid=,ppid=,rss=,command="], {
+        encoding: "utf-8",
+        maxBuffer: 10 * 1024 * 1024,
+    });
+    const rows = [];
+    for (const line of raw.split("\n")) {
+        const match = line.match(/^\s*(\d+)\s+(\d+)\s+(\d+)\s+(.+)$/);
+        if (!match)
+            continue;
+        rows.push({
+            pid: Number(match[1]),
+            ppid: Number(match[2]),
+            rssKb: Number(match[3]),
+            command: match[4] ?? "",
+        });
+    }
+    return rows;
+}
+function classifyCleanupTarget(command, includeGlobalCodesift) {
+    const node = String.raw `(?:node|\S*/node)`;
+    const npm = String.raw `(?:npm|\S*/npm)`;
+    if (command === "" || /(?:^|\s)codesift\s+cleanup-processes(?:\s|$)/.test(command))
+        return null;
+    if (new RegExp(`^${node}\\s+/Users/\\S+/DEV/codesift-mcp/dist/server\\.js(?:\\s|$)`).test(command)) {
+        return "legacy-dev-dist-server";
+    }
+    if (new RegExp(`^${npm}\\s+exec\\s+chrome-devtools-mcp(?:@\\S+)?(?:\\s|$)`).test(command) ||
+        /^(?:\S*\/)?chrome-devtools-mcp(?:\s|$)/.test(command)) {
+        return "chrome-devtools-mcp";
+    }
+    if (new RegExp(`^${node}\\s+\\S*chrome-devtools-mcp/\\S*/watchdog/main\\.js(?:\\s|$)`).test(command)) {
+        return "chrome-devtools-watchdog";
+    }
+    if (new RegExp(`^${npm}\\s+exec\\s+@sentry/mcp-server(?:@\\S+)?(?:\\s|$)`).test(command)) {
+        return "sentry-mcp";
+    }
+    if (new RegExp(`^${npm}\\s+exec\\s+@playwright/mcp(?:@\\S+)?(?:\\s|$)`).test(command)) {
+        return "playwright-mcp";
+    }
+    if (includeGlobalCodesift &&
+        new RegExp(`^(?:${node}\\s+)?/Users/\\S+/.npm-global/bin/codesift-mcp(?:\\s|$)`).test(command)) {
+        return "global-codesift-mcp";
+    }
+    return null;
+}
+function currentProcessCommand(pid) {
+    try {
+        return execFileSync("ps", ["-p", String(pid), "-o", "command="], {
+            encoding: "utf-8",
+            maxBuffer: 1024 * 1024,
+        }).trim() || null;
+    }
+    catch {
+        return null;
+    }
+}
+async function handleCleanupProcesses(_args, flags) {
+    const dryRun = getBoolFlag(flags, "dry-run") === true;
+    const includeGlobalCodesift = getBoolFlag(flags, "global-codesift") === true;
+    const rows = listProcesses();
+    const targets = rows
+        .map((row) => ({ ...row, reason: classifyCleanupTarget(row.command, includeGlobalCodesift) }))
+        .filter((row) => row.reason !== null);
+    const beforeMb = targets.reduce((sum, row) => sum + row.rssKb, 0) / 1024;
+    const killed = [];
+    const failed = [];
+    if (!dryRun) {
+        for (const row of targets) {
+            try {
+                const current = currentProcessCommand(row.pid);
+                if (current !== row.command || classifyCleanupTarget(current, includeGlobalCodesift) !== row.reason) {
+                    throw new Error("process identity changed before kill");
+                }
+                process.kill(row.pid, "SIGKILL");
+                killed.push(row);
+            }
+            catch (err) {
+                failed.push({ ...row, error: err instanceof Error ? err.message : String(err) });
+            }
+        }
+    }
+    const byReason = {};
+    for (const row of targets) {
+        byReason[row.reason] ??= { count: 0, rss_mb: 0 };
+        byReason[row.reason].count += 1;
+        byReason[row.reason].rss_mb += row.rssKb / 1024;
+    }
+    for (const value of Object.values(byReason)) {
+        value.rss_mb = Number(value.rss_mb.toFixed(1));
+    }
+    output({
+        dry_run: dryRun,
+        include_global_codesift: includeGlobalCodesift,
+        matched: targets.length,
+        killed: dryRun ? 0 : killed.length,
+        failed: failed.length,
+        matched_rss_mb: Number(beforeMb.toFixed(1)),
+        by_reason: byReason,
+        failed_pids: failed.map((row) => ({ pid: row.pid, reason: row.reason, error: row.error })),
+    }, flags);
+}
+export { handlePrune, handleCleanupProcesses };
+//# sourceMappingURL=commands-maintenance.js.map

package/dist/cli/commands-maintenance.js.map

@@ -0,0 +1 @@
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package/dist/cli/commands-query.d.ts

@@ -0,0 +1,21 @@
+import type { Flags } from "./args.js";
+declare function handleSearch(args: string[], flags: Flags): Promise<void>;
+declare function handleSymbols(args: string[], flags: Flags): Promise<void>;
+declare function handleTree(args: string[], flags: Flags): Promise<void>;
+declare function handleOutline(args: string[], flags: Flags): Promise<void>;
+declare function handleRepoOutline(args: string[], flags: Flags): Promise<void>;
+declare function handleSymbol(args: string[], flags: Flags): Promise<void>;
+declare function handleSymbolsBatch(args: string[], flags: Flags): Promise<void>;
+declare function handleFind(args: string[], flags: Flags): Promise<void>;
+declare function handleRefs(args: string[], flags: Flags): Promise<void>;
+declare function handleTrace(args: string[], flags: Flags): Promise<void>;
+declare function handleImpact(args: string[], flags: Flags): Promise<void>;
+declare function handleContext(args: string[], flags: Flags): Promise<void>;
+declare function handleKnowledgeMap(args: string[], flags: Flags): Promise<void>;
+declare function handleDiff(args: string[], flags: Flags): Promise<void>;
+declare function handleChanged(args: string[], flags: Flags): Promise<void>;
+declare function handleRetrieve(args: string[], flags: Flags): Promise<void>;
+declare function handleStats(_args: string[], flags: Flags): Promise<void>;
+declare function handleGenerateClaudeMd(args: string[], flags: Flags): Promise<void>;
+export { handleSearch, handleSymbols, handleTree, handleOutline, handleRepoOutline, handleSymbol, handleSymbolsBatch, handleFind, handleRefs, handleTrace, handleImpact, handleContext, handleKnowledgeMap, handleDiff, handleChanged, handleRetrieve, handleStats, handleGenerateClaudeMd, };
+//# sourceMappingURL=commands-query.d.ts.map

package/dist/cli/commands-query.d.ts.map

@@ -0,0 +1 @@
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