@luisarg/memory-mcp 0.1.1 → 0.1.3

package/cordis.patch.yml

@@ -10,8 +10,10 @@
       config:
         serverName: memory
         transport: stdio
-        command: uv
-        args: [run, --directory, !!js process.env.DSH_MEMORY_SERVER_DIR ?? dshHomePath('memory-vault-server'), python, server.py]
+        # launcher.mjs (bundled with the server): `uv run` when uv is on PATH,
+        # else a pip-managed .venv (python3 -m venv + pip install -r requirements.txt)
+        command: !!js process.execPath
+        args: [!!js "(process.env.DSH_MEMORY_SERVER_DIR ?? dshHomePath('memory-vault-server')) + '/launcher.mjs'"]
         env:
           MEMORY_PATH: !!js process.env.DSH_MEMORY_PATH ?? dshHomePath('memory-vault')
           UV_CACHE_DIR: /tmp/uv-cache

package/dist/index.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"index.d.ts","names":[],"sources":["../src/index.ts"],"sourcesContent":[],"mappings":";;;;cAOa,IAAA;UAEI,MAAA;EAFJ,UAAI,EAAA,MAAA;EAEA,SAAM,EAAA,MAAA;AAKvB;AA6BgB,cA7BH,MA6Bc,EA7BN,MA6BuB,CA7BhB,MA6BsB,CAAA;iBAAlC,KAAA,MAAW,iBAAiB"}
+{"version":3,"file":"index.d.ts","names":[],"sources":["../src/index.ts"],"sourcesContent":[],"mappings":";;;;cAOa,IAAA;UAEI,MAAA;EAFJ,UAAI,EAAA,MAAA;EAEA,SAAM,EAAA,MAAA;AAKvB;AAwCgB,cAxCH,MAwCc,EAxCN,MAwCuB,CAxChB,MAwCsB,CAAA;iBAAlC,KAAA,MAAW,iBAAiB"}

package/dist/index.js

@@ -30,11 +30,23 @@ function ensure(target, bundled, key) {
 	cpSync(bundled, target, { recursive: true });
 	return true;
 }
+/** Copy one bundled file into `target` when missing (upgrades add files 0.1.1 → 0.1.2). */
+function ensureFile(target, bundled, file) {
+	const dest = join(target, file);
+	if (existsSync(dest)) return false;
+	const src = join(bundled, file);
+	if (!existsSync(src)) return false;
+	mkdirSync(target, { recursive: true });
+	cpSync(src, dest);
+	return true;
+}
 function apply(ctx, config) {
 	const serverDir = resolveUnderHome(config.serverDir, "memory-vault-server");
 	const memoryPath = resolveUnderHome(config.memoryPath, "memory-vault");
 	if (ensure(serverDir, join(packageRoot, "server"), "server.py")) console.log(`[memory-mcp] installed memory-vault-server -> ${serverDir}`);
 	if (ensure(memoryPath, join(packageRoot, "vault"), "type-registry.yaml")) console.log(`[memory-mcp] installed vault starter -> ${memoryPath}`);
+	const bundled = join(packageRoot, "server");
+	for (const file of ["launcher.mjs", "requirements.txt"]) if (ensureFile(serverDir, bundled, file)) console.log(`[memory-mcp] installed ${file} -> ${serverDir}`);
 	if (!existsSync(join(serverDir, "server.py"))) console.warn(`[memory-mcp] memory-vault-server not found at ${serverDir} and not bundled — set DSH_MEMORY_SERVER_DIR (or run \`node scripts/bundle-assets.mjs\` in a checkout)`);
 }
 

package/dist/index.js.map

@@ -1 +1 @@
-{"version":3,"file":"index.js","names":["Config: Schema<Config>"],"sources":["../src/index.ts"],"sourcesContent":["import { cpSync, existsSync, mkdirSync } from 'node:fs'\nimport { homedir } from 'node:os'\nimport { dirname, isAbsolute, join } from 'node:path'\nimport { fileURLToPath } from 'node:url'\nimport type { Context } from '@deepseek-ai/cordis'\nimport Schema from '@deepseek-ai/schemastery'\n\nexport const name = 'memory-mcp'\n\nexport interface Config {\n  memoryPath: string\n  serverDir: string\n}\n\nexport const Config: Schema<Config> = Schema.object({\n  memoryPath: Schema.string().default(process.env.DSH_MEMORY_PATH ?? ''),\n  serverDir: Schema.string().default(process.env.DSH_MEMORY_SERVER_DIR ?? ''),\n})\n\nconst packageRoot = dirname(dirname(fileURLToPath(import.meta.url)))\n\n/** Harness home, resolved like the harness itself ($DSH_HOME, or ~/.dsh). */\nfunction dshHome(): string {\n  const env = process.env.DSH_HOME?.trim()\n  return env && env.length > 0 ? env : join(homedir(), '.dsh')\n}\n\n/** Absolute paths stay; empty/relative values resolve under the harness home. */\nfunction resolveUnderHome(value: string, segment: string): string {\n  const v = value.trim()\n  if (v.length === 0) return join(dshHome(), segment)\n  return isAbsolute(v) ? v : join(dshHome(), v)\n}\n\n/** Copy the bundled dir into `target` when `key` is missing there. */\nfunction ensure(target: string, bundled: string, key: string): boolean {\n  if (existsSync(join(target, key))) return false\n  if (!existsSync(bundled)) return false\n  mkdirSync(target, { recursive: true })\n  cpSync(bundled, target, { recursive: true })\n  return true\n}\n\nexport function apply(ctx: Context, config: Config) {\n  const serverDir = resolveUnderHome(config.serverDir, 'memory-vault-server')\n  const memoryPath = resolveUnderHome(config.memoryPath, 'memory-vault')\n\n  // Self-contained install: first boot copies the bundled server and vault\n  // starter under the harness home when they are missing. Env-overridden\n  // paths are respected (never overwritten, never copied over).\n  if (ensure(serverDir, join(packageRoot, 'server'), 'server.py')) {\n    console.log(`[memory-mcp] installed memory-vault-server -> ${serverDir}`)\n  }\n  if (ensure(memoryPath, join(packageRoot, 'vault'), 'type-registry.yaml')) {\n    console.log(`[memory-mcp] installed vault starter -> ${memoryPath}`)\n  }\n  if (!existsSync(join(serverDir, 'server.py'))) {\n    console.warn(\n      `[memory-mcp] memory-vault-server not found at ${serverDir} and not bundled — ` +\n      'set DSH_MEMORY_SERVER_DIR (or run `node scripts/bundle-assets.mjs` in a checkout)',\n    )\n  }\n}\n"],"mappings":";;;;;;;AAOA,MAAa,OAAO;AAOpB,MAAaA,SAAyB,OAAO,OAAO;CAClD,YAAY,OAAO,QAAQ,CAAC,QAAQ,QAAQ,IAAI,mBAAmB,GAAG;CACtE,WAAW,OAAO,QAAQ,CAAC,QAAQ,QAAQ,IAAI,yBAAyB,GAAG;CAC5E,CAAC;AAEF,MAAM,cAAc,QAAQ,QAAQ,cAAc,OAAO,KAAK,IAAI,CAAC,CAAC;;AAGpE,SAAS,UAAkB;CACzB,MAAM,MAAM,QAAQ,IAAI,UAAU,MAAM;AACxC,QAAO,OAAO,IAAI,SAAS,IAAI,MAAM,KAAK,SAAS,EAAE,OAAO;;;AAI9D,SAAS,iBAAiB,OAAe,SAAyB;CAChE,MAAM,IAAI,MAAM,MAAM;AACtB,KAAI,EAAE,WAAW,EAAG,QAAO,KAAK,SAAS,EAAE,QAAQ;AACnD,QAAO,WAAW,EAAE,GAAG,IAAI,KAAK,SAAS,EAAE,EAAE;;;AAI/C,SAAS,OAAO,QAAgB,SAAiB,KAAsB;AACrE,KAAI,WAAW,KAAK,QAAQ,IAAI,CAAC,CAAE,QAAO;AAC1C,KAAI,CAAC,WAAW,QAAQ,CAAE,QAAO;AACjC,WAAU,QAAQ,EAAE,WAAW,MAAM,CAAC;AACtC,QAAO,SAAS,QAAQ,EAAE,WAAW,MAAM,CAAC;AAC5C,QAAO;;AAGT,SAAgB,MAAM,KAAc,QAAgB;CAClD,MAAM,YAAY,iBAAiB,OAAO,WAAW,sBAAsB;CAC3E,MAAM,aAAa,iBAAiB,OAAO,YAAY,eAAe;AAKtE,KAAI,OAAO,WAAW,KAAK,aAAa,SAAS,EAAE,YAAY,CAC7D,SAAQ,IAAI,iDAAiD,YAAY;AAE3E,KAAI,OAAO,YAAY,KAAK,aAAa,QAAQ,EAAE,qBAAqB,CACtE,SAAQ,IAAI,2CAA2C,aAAa;AAEtE,KAAI,CAAC,WAAW,KAAK,WAAW,YAAY,CAAC,CAC3C,SAAQ,KACN,iDAAiD,UAAU,wGAE5D"}
+{"version":3,"file":"index.js","names":["Config: Schema<Config>"],"sources":["../src/index.ts"],"sourcesContent":["import { cpSync, existsSync, mkdirSync } from 'node:fs'\nimport { homedir } from 'node:os'\nimport { dirname, isAbsolute, join } from 'node:path'\nimport { fileURLToPath } from 'node:url'\nimport type { Context } from '@deepseek-ai/cordis'\nimport Schema from '@deepseek-ai/schemastery'\n\nexport const name = 'memory-mcp'\n\nexport interface Config {\n  memoryPath: string\n  serverDir: string\n}\n\nexport const Config: Schema<Config> = Schema.object({\n  memoryPath: Schema.string().default(process.env.DSH_MEMORY_PATH ?? ''),\n  serverDir: Schema.string().default(process.env.DSH_MEMORY_SERVER_DIR ?? ''),\n})\n\nconst packageRoot = dirname(dirname(fileURLToPath(import.meta.url)))\n\n/** Harness home, resolved like the harness itself ($DSH_HOME, or ~/.dsh). */\nfunction dshHome(): string {\n  const env = process.env.DSH_HOME?.trim()\n  return env && env.length > 0 ? env : join(homedir(), '.dsh')\n}\n\n/** Absolute paths stay; empty/relative values resolve under the harness home. */\nfunction resolveUnderHome(value: string, segment: string): string {\n  const v = value.trim()\n  if (v.length === 0) return join(dshHome(), segment)\n  return isAbsolute(v) ? v : join(dshHome(), v)\n}\n\n/** Copy the bundled dir into `target` when `key` is missing there. */\nfunction ensure(target: string, bundled: string, key: string): boolean {\n  if (existsSync(join(target, key))) return false\n  if (!existsSync(bundled)) return false\n  mkdirSync(target, { recursive: true })\n  cpSync(bundled, target, { recursive: true })\n  return true\n}\n\n/** Copy one bundled file into `target` when missing (upgrades add files 0.1.1 → 0.1.2). */\nfunction ensureFile(target: string, bundled: string, file: string): boolean {\n  const dest = join(target, file)\n  if (existsSync(dest)) return false\n  const src = join(bundled, file)\n  if (!existsSync(src)) return false\n  mkdirSync(target, { recursive: true })\n  cpSync(src, dest)\n  return true\n}\n\nexport function apply(ctx: Context, config: Config) {\n  const serverDir = resolveUnderHome(config.serverDir, 'memory-vault-server')\n  const memoryPath = resolveUnderHome(config.memoryPath, 'memory-vault')\n\n  // Self-contained install: first boot copies the bundled server and vault\n  // starter under the harness home when they are missing. Env-overridden\n  // paths are respected (never overwritten, never copied over).\n  if (ensure(serverDir, join(packageRoot, 'server'), 'server.py')) {\n    console.log(`[memory-mcp] installed memory-vault-server -> ${serverDir}`)\n  }\n  if (ensure(memoryPath, join(packageRoot, 'vault'), 'type-registry.yaml')) {\n    console.log(`[memory-mcp] installed vault starter -> ${memoryPath}`)\n  }\n  // launcher.mjs runs the server via uv or the pip-venv fallback; upgrades of\n  // existing installs (server.py already present) still need the new files.\n  const bundled = join(packageRoot, 'server')\n  for (const file of ['launcher.mjs', 'requirements.txt']) {\n    if (ensureFile(serverDir, bundled, file)) {\n      console.log(`[memory-mcp] installed ${file} -> ${serverDir}`)\n    }\n  }\n  if (!existsSync(join(serverDir, 'server.py'))) {\n    console.warn(\n      `[memory-mcp] memory-vault-server not found at ${serverDir} and not bundled — ` +\n      'set DSH_MEMORY_SERVER_DIR (or run `node scripts/bundle-assets.mjs` in a checkout)',\n    )\n  }\n}\n"],"mappings":";;;;;;;AAOA,MAAa,OAAO;AAOpB,MAAaA,SAAyB,OAAO,OAAO;CAClD,YAAY,OAAO,QAAQ,CAAC,QAAQ,QAAQ,IAAI,mBAAmB,GAAG;CACtE,WAAW,OAAO,QAAQ,CAAC,QAAQ,QAAQ,IAAI,yBAAyB,GAAG;CAC5E,CAAC;AAEF,MAAM,cAAc,QAAQ,QAAQ,cAAc,OAAO,KAAK,IAAI,CAAC,CAAC;;AAGpE,SAAS,UAAkB;CACzB,MAAM,MAAM,QAAQ,IAAI,UAAU,MAAM;AACxC,QAAO,OAAO,IAAI,SAAS,IAAI,MAAM,KAAK,SAAS,EAAE,OAAO;;;AAI9D,SAAS,iBAAiB,OAAe,SAAyB;CAChE,MAAM,IAAI,MAAM,MAAM;AACtB,KAAI,EAAE,WAAW,EAAG,QAAO,KAAK,SAAS,EAAE,QAAQ;AACnD,QAAO,WAAW,EAAE,GAAG,IAAI,KAAK,SAAS,EAAE,EAAE;;;AAI/C,SAAS,OAAO,QAAgB,SAAiB,KAAsB;AACrE,KAAI,WAAW,KAAK,QAAQ,IAAI,CAAC,CAAE,QAAO;AAC1C,KAAI,CAAC,WAAW,QAAQ,CAAE,QAAO;AACjC,WAAU,QAAQ,EAAE,WAAW,MAAM,CAAC;AACtC,QAAO,SAAS,QAAQ,EAAE,WAAW,MAAM,CAAC;AAC5C,QAAO;;;AAIT,SAAS,WAAW,QAAgB,SAAiB,MAAuB;CAC1E,MAAM,OAAO,KAAK,QAAQ,KAAK;AAC/B,KAAI,WAAW,KAAK,CAAE,QAAO;CAC7B,MAAM,MAAM,KAAK,SAAS,KAAK;AAC/B,KAAI,CAAC,WAAW,IAAI,CAAE,QAAO;AAC7B,WAAU,QAAQ,EAAE,WAAW,MAAM,CAAC;AACtC,QAAO,KAAK,KAAK;AACjB,QAAO;;AAGT,SAAgB,MAAM,KAAc,QAAgB;CAClD,MAAM,YAAY,iBAAiB,OAAO,WAAW,sBAAsB;CAC3E,MAAM,aAAa,iBAAiB,OAAO,YAAY,eAAe;AAKtE,KAAI,OAAO,WAAW,KAAK,aAAa,SAAS,EAAE,YAAY,CAC7D,SAAQ,IAAI,iDAAiD,YAAY;AAE3E,KAAI,OAAO,YAAY,KAAK,aAAa,QAAQ,EAAE,qBAAqB,CACtE,SAAQ,IAAI,2CAA2C,aAAa;CAItE,MAAM,UAAU,KAAK,aAAa,SAAS;AAC3C,MAAK,MAAM,QAAQ,CAAC,gBAAgB,mBAAmB,CACrD,KAAI,WAAW,WAAW,SAAS,KAAK,CACtC,SAAQ,IAAI,0BAA0B,KAAK,MAAM,YAAY;AAGjE,KAAI,CAAC,WAAW,KAAK,WAAW,YAAY,CAAC,CAC3C,SAAQ,KACN,iDAAiD,UAAU,wGAE5D"}

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@luisarg/memory-mcp",
-  "version": "0.1.1",
+  "version": "0.1.3",
   "type": "module",
   "description": "DSH MCP client for the memory vault",
   "repository": {

package/server/launcher.mjs

@@ -0,0 +1,73 @@
+// memory-vault-server launcher — run `server.py` with uv when uv is on PATH,
+// otherwise bootstrap a pip venv (.venv + requirements.txt) and run with that
+// python. Used by both DSH launch points (memory-mcp cordis patch, memory-auto
+// digest) so the fallback decision lives in exactly one place.
+//
+// stdout is the MCP channel of the spawned server — never print to it here.
+// All progress/errors go to stderr.
+//
+// ponytail: fallback triggers only when the `uv` binary is absent, not when
+// `uv run` fails (e.g. offline with an empty cache). If that ever matters,
+// upgrade path: on uv run exit != 0, retry through the pip branch below.
+
+import { spawn, spawnSync } from 'node:child_process'
+import { existsSync } from 'node:fs'
+import { tmpdir } from 'node:os'
+import { dirname, join } from 'node:path'
+import { fileURLToPath, pathToFileURL } from 'node:url'
+
+const DIR = dirname(fileURLToPath(import.meta.url))
+
+/** Pure decision: which command runs the server, given uv presence. */
+export function resolveRunner(hasUv, dir = DIR, platform = process.platform) {
+  if (hasUv) return { command: 'uv', args: ['run', '--directory', dir, 'python', 'server.py'] }
+  const pyBin = join(dir, platform === 'win32' ? '.venv/Scripts/python.exe' : '.venv/bin/python')
+  return { command: pyBin, args: ['server.py'] }
+}
+
+export function hasUv() {
+  return spawnSync('uv', ['--version'], { stdio: 'ignore' }).status === 0
+}
+
+/** Ensure a runnable venv with the server's deps installed (pip branch only). */
+export function ensurePipEnv(dir = DIR, platform = process.platform) {
+  const pyBin = join(dir, platform === 'win32' ? '.venv/Scripts/python.exe' : '.venv/bin/python')
+  const venvCmd = platform === 'win32' ? 'py' : 'python3'
+  if (!existsSync(pyBin)) {
+    console.error('[memory-vault-server] uv not found — creating fallback venv with ' + venvCmd)
+    // stdout is the MCP channel: keep install output off it.
+    const created = spawnSync(venvCmd, ['-m', 'venv', join(dir, '.venv')], { stdio: ['ignore', 'ignore', 'inherit'] })
+    if (created.status !== 0) {
+      console.error(`[memory-vault-server] venv creation failed (exit ${created.status}) — install uv or fix ${venvCmd}`)
+      process.exit(created.status ?? 1)
+    }
+  }
+  const depsOk = spawnSync(pyBin, ['-c', 'import mcp, yaml'], { stdio: 'ignore' }).status === 0
+  if (!depsOk) {
+    console.error('[memory-vault-server] fallback venv missing deps — pip install -r requirements.txt')
+    const pip = spawnSync(pyBin, ['-m', 'pip', 'install', '--quiet', '-r', join(dir, 'requirements.txt')], { stdio: ['ignore', 'ignore', 'inherit'] })
+    if (pip.status !== 0) {
+      console.error(`[memory-vault-server] pip install failed (exit ${pip.status}) — install uv, fix the network, or run the pip install manually`)
+      process.exit(pip.status ?? 1)
+    }
+  }
+  return pyBin
+}
+
+function main() {
+  const withUv = hasUv()
+  const { command, args } = resolveRunner(withUv)
+  if (!withUv) ensurePipEnv()
+  // Default the uv cache under the OS temp dir (Windows has no /tmp); an
+  // explicit UV_CACHE_DIR from the patch layer or env still wins.
+  const env = { UV_CACHE_DIR: join(tmpdir(), 'uv-cache'), ...process.env }
+  const child = spawn(command, args, { cwd: DIR, env, stdio: 'inherit' })
+  for (const sig of ['SIGTERM', 'SIGINT']) process.on(sig, () => child.kill(sig))
+  child.on('error', (err) => {
+    console.error(`[memory-vault-server] spawn failed (${command}): ${err.message}`)
+    process.exit(1)
+  })
+  child.on('exit', (code, signal) => process.exit(code ?? (signal ? 1 : 0)))
+}
+
+if (process.argv[1] && import.meta.url === pathToFileURL(process.argv[1]).href) main()

package/server/rebuild_index.py

@@ -0,0 +1,191 @@
+"""Rebuild the SQLite FTS5 index from the OKF Markdown bundle (index-only).
+
+Walks `projects/<project>/<type>/*.md` and `raw/*.md`, parses each file and
+inserts rows directly into SQLite. Markdown stays the source of truth: this
+script never rewrites .md files (upsert_entry's write path would duplicate
+them with today's date on a fresh DB).
+
+Idempotent: row ids derive from file paths, dedup keys from content, so
+re-running converges. Run after importing a bundle into a new vault dir
+(memory.db* may be deleted first; the script also works on a populated DB):
+
+    uv run --directory memory-vault-server python rebuild_index.py \
+        --memory-path /path/to/vault
+
+DB-only data (profiles) is NOT covered — migrate profiles separately.
+"""
+
+from __future__ import annotations
+
+import argparse
+import hashlib
+import os
+import sys
+from pathlib import Path
+
+_store_mod = None  # set in main() once MEMORY_PATH points at the target bundle
+
+
+def _id_for(relpath: Path) -> str:
+    """Stable row id derived from the file path (idempotent re-runs)."""
+    digest = hashlib.sha1(str(relpath).encode()).hexdigest()[:24]
+    return f"rebuild-{digest}"
+
+
+def _collect(memory_path: Path):
+    """Walk the bundle -> (entries, errors); entries are
+    (singular, project, relpath, parsed) tuples, DB-only types skipped."""
+    entries: list[tuple[str, str, Path, dict]] = []
+    errors: list[str] = []
+    dir_to_singular = _store_mod._DIR_TO_SINGULAR
+    parse = _store_mod._parse_okf_file
+
+    def handle(path: Path, parsed: dict | None, default_project: str, singular: str):
+        if parsed is None:
+            errors.append(f"unparseable: {path.relative_to(memory_path)}")
+            return
+        # Defensive: trust the directory, not the parsed label.
+        parsed["entry_type"] = singular
+        parsed["project"] = parsed.get("project") or default_project
+        entries.append((singular, parsed["project"], path.relative_to(memory_path), parsed))
+
+    projects_dir = memory_path / "projects"
+    if projects_dir.is_dir():
+        # Projects may nest (e.g. `@deepseek-ai/dsh-root`): any directory whose
+        # name is a type dir is indexed; its project is the dir path below
+        # `projects/`, joined with "/".
+        def scan(prefix: Path, project: str):
+            for d in sorted(child for child in prefix.iterdir() if child.is_dir()):
+                singular = dir_to_singular.get(d.name)
+                if singular is None:
+                    if d.name != ".obsidian":
+                        scan(d, f"{project}/{d.name}" if project else d.name)
+                    continue
+                if singular == "profile":
+                    continue
+                for f in sorted(d.glob("*.md")):
+                    if f.name == "index.md":
+                        continue
+                    handle(f, parse(f), project, singular)
+
+        for proj_dir in sorted(p for p in projects_dir.iterdir() if p.is_dir()):
+            scan(proj_dir, proj_dir.name)
+
+    raw_dir = memory_path / "raw"
+    if raw_dir.is_dir():
+        for f in sorted(raw_dir.glob("*.md")):
+            handle(f, parse(f), "", "source")
+
+    return entries, errors
+
+
+def rebuild(memory_path: Path) -> tuple[int, int, list[str]]:
+    """Insert all bundle entries into the index -> (inserted, updated, errors)."""
+    store = _store_mod.MemoryStore(storage_path=memory_path)
+    store.initialize()
+
+    entries, errors = _collect(memory_path)
+    if not entries:
+        print("No entries found in bundle; nothing to do.", file=sys.stderr)
+        return 0, 0, errors
+
+    n_inserted = n_updated = 0
+    for singular, project, relpath, e in entries:
+        try:
+            dedup_key = (
+                store._make_dedup_key(singular, project, e["content"])
+                if singular != "source"
+                else _id_for(relpath)
+            )
+            existing = store.db.execute(
+                "SELECT id FROM entries WHERE dedup_key = ?", (dedup_key,)
+            ).fetchone()
+            if existing:
+                if existing["id"] != _id_for(relpath):
+                    # Same content already indexed (bundle duplicates collapse):
+                    # adopt this file's id so re-runs converge, keep row content.
+                    store.db.execute(
+                        "UPDATE entries SET id = ?, created_at = ?, updated_at = ? WHERE dedup_key = ?",
+                        (_id_for(relpath), e["created_at"], e["updated_at"], dedup_key),
+                    )
+                    store.db.commit()
+                n_updated += 1
+                continue
+            store._insert_row(
+                _id_for(relpath),
+                singular,
+                project,
+                e["content"],
+                e["tags"],
+                float(e["confidence"] or 1.0),
+                e["openspec_change_id"],
+                dedup_key,
+                e["created_at"],
+                e["updated_at"],
+            )
+            n_inserted += 1
+        except Exception as exc:  # noqa: BLE001 — one bad file must not stop the rebuild
+            errors.append(f"failed: {project}/{relpath}: {exc}")
+    return n_inserted, n_updated, errors
+
+
+def regen_missing_indexes(memory_path: Path, store) -> int:
+    """Regenerate `<project>/index.md` only where it is missing (nested too)."""
+    projects_dir = memory_path / "projects"
+    if not projects_dir.is_dir():
+        return 0
+    n = 0
+
+    def scan(prefix: Path):
+        for d in sorted(child for child in prefix.iterdir() if child.is_dir()):
+            if d.name in _store_mod._DIR_TO_SINGULAR or d.name == ".obsidian":
+                continue  # type dir or editor cache — not a project
+            if not (d / "index.md").exists():
+                project = str(d.relative_to(projects_dir)).replace(os.sep, "/")
+                store._regenerate_project_index(project)
+                n += 1
+            scan(d)
+
+    for proj_dir in sorted(p for p in projects_dir.iterdir() if p.is_dir()):
+        if not (proj_dir / "index.md").exists():
+            store._regenerate_project_index(proj_dir.name)
+            n += 1
+        scan(proj_dir)
+    return n
+
+
+def main(argv: list[str] | None = None) -> int:
+    global _store_mod
+    parser = argparse.ArgumentParser(description="Rebuild SQLite index from OKF bundle")
+    parser.add_argument(
+        "--memory-path",
+        default=None,
+        help="OKF bundle directory (default: $MEMORY_PATH or repo memory-vault)",
+    )
+    args = parser.parse_args(argv)
+
+    # store.py builds its type maps from MEMORY_PATH at import time — point it
+    # at the target bundle before importing.
+    if args.memory_path:
+        os.environ["MEMORY_PATH"] = str(Path(args.memory_path).resolve())
+    import store as _store_mod
+
+    memory_path = Path(os.environ.get("MEMORY_PATH", "")).resolve()
+    if not memory_path.is_dir():
+        print(f"error: {memory_path} is not a directory", file=sys.stderr)
+        return 2
+
+    print(f"Rebuilding index from {memory_path} ...")
+    n_ins, n_upd, errors = rebuild(memory_path)
+    store = _store_mod.MemoryStore(storage_path=memory_path)
+    store.initialize()
+    n_index = regen_missing_indexes(memory_path, store)
+    print(f"Inserted: {n_ins}, already-indexed: {n_upd}, index.md regenerated: {n_index}")
+    for err in errors:
+        print(f"  {err}", file=sys.stderr)
+    print(f"Errors: {len(errors)}")
+    return 0 if not errors else 1
+
+
+if __name__ == "__main__":
+    raise SystemExit(main())

package/server/requirements.txt

@@ -0,0 +1,4 @@
+# Mirror of the dependencies in pyproject.toml — keep in sync by hand.
+# Used only by launcher.mjs' pip fallback on hosts without uv.
+mcp>=1.2.0
+PyYAML>=6.0

package/server/store.py

@@ -263,7 +263,10 @@ class MemoryStore:
         db_path = self.storage_path / "memory.db"
         if db_path.exists() and db_path.stat().st_size > 0:
             try:
-                test_conn = sqlite3.connect(str(db_path))
+                # timeout=30: with WAL a live vault may be written by another
+                # client (DSH + opencode). Without it the probe waits only 5 s
+                # and a busy lock surfaces as "corrupt database".
+                test_conn = sqlite3.connect(str(db_path), timeout=30)
                 row = test_conn.execute("PRAGMA integrity_check").fetchone()
                 test_conn.close()
                 if row[0].lower() != "ok":
@@ -271,7 +274,7 @@ class MemoryStore:
             except sqlite3.DatabaseError as e:
                 raise RuntimeError(f"corrupt database: {e}") from e
 
-        self._db = sqlite3.connect(str(db_path))
+        self._db = sqlite3.connect(str(db_path), timeout=30)
         self._db.row_factory = sqlite3.Row
         self.db.execute("PRAGMA journal_mode=WAL")
         self.db.execute("PRAGMA foreign_keys=ON")