fix: align WAL multi-surface DB safety

- align app and standalone MCP busy-timeout and retry behavior
- guard live DB dev and restore flows
- document WAL maintenance boundaries

apps/mcp-server-standalone/README.md

@@ -28,6 +28,7 @@ Important contract:
 - exact versions are only for release/debug reproducibility
 - standalone MCP reads and writes node data directly
 - standalone MCP does not own chunking, embeddings, or live schema migration on an existing DB
+- standalone MCP and the app use SQLite WAL; normal short reads/writes can coexist, while restore/replace/checkpoint/delete-WAL maintenance requires all DB owners to be closed first
 
 ## Configure Claude Code / Claude Desktop
 

apps/mcp-server-standalone/services/edgeService.js

@@ -1,6 +1,6 @@
 'use strict';
 
-const { query, getDb } = require('./sqlite-client');
+const { query, getDb, runWithBusyRetry } = require('./sqlite-client');
 
 /**
  * Get all edges.
@@ -74,12 +74,14 @@ function createEdge(edgeData) {
     VALUES (?, ?, ?, ?, ?)
   `);
 
-  const result = stmt.run(
-    from_node_id,
-    to_node_id,
-    JSON.stringify(context),
-    source,
-    now
+  const result = runWithBusyRetry(() => stmt.run(
+      from_node_id,
+      to_node_id,
+      JSON.stringify(context),
+      source,
+      now
+    ),
+    'createEdge'
   );
 
   const edgeId = Number(result.lastInsertRowid);
@@ -109,14 +111,14 @@ function updateEdge(id, updates) {
     };
 
     const stmt = db.prepare('UPDATE edges SET context = ? WHERE id = ?');
-    stmt.run(JSON.stringify(newContext), id);
+    runWithBusyRetry(() => stmt.run(JSON.stringify(newContext), id), 'updateEdge');
   } else if (contextUpdates) {
     const newContext = {
       ...existing.context,
       ...contextUpdates
     };
     const stmt = db.prepare('UPDATE edges SET context = ? WHERE id = ?');
-    stmt.run(JSON.stringify(newContext), id);
+    runWithBusyRetry(() => stmt.run(JSON.stringify(newContext), id), 'updateEdge');
   }
 
   return getEdgeById(id);

apps/mcp-server-standalone/services/sqlite-client.js

@@ -89,11 +89,11 @@ function initDatabase() {
 
   db = new Database(dbPath);
 
-  // Configure SQLite for performance
+  // Configure SQLite for WAL-first app/MCP coexistence.
   db.pragma('journal_mode = WAL');
   db.pragma('synchronous = NORMAL');
   db.pragma('cache_size = 5000');
-  db.pragma('busy_timeout = 5000');
+  db.pragma('busy_timeout = 10000');
 
   validateExistingRahSchema(db);
 
@@ -254,19 +254,21 @@ function getDb() {
  * Execute a query and return rows.
  */
 function query(sql, params = []) {
-  const database = getDb();
-  const stmt = database.prepare(sql);
+  return runWithBusyRetry(() => {
+    const database = getDb();
+    const stmt = database.prepare(sql);
 
-  const sqlLower = sql.trim().toLowerCase();
-  if (sqlLower.startsWith('select') || sqlLower.startsWith('with') || sqlLower.startsWith('pragma') || sqlLower.includes('returning')) {
-    return params.length > 0 ? stmt.all(...params) : stmt.all();
-  } else {
-    const result = params.length > 0 ? stmt.run(...params) : stmt.run();
-    return {
-      changes: result.changes,
-      lastInsertRowid: Number(result.lastInsertRowid)
-    };
-  }
+    const sqlLower = sql.trim().toLowerCase();
+    if (sqlLower.startsWith('select') || sqlLower.startsWith('with') || sqlLower.startsWith('pragma') || sqlLower.includes('returning')) {
+      return params.length > 0 ? stmt.all(...params) : stmt.all();
+    } else {
+      const result = params.length > 0 ? stmt.run(...params) : stmt.run();
+      return {
+        changes: result.changes,
+        lastInsertRowid: Number(result.lastInsertRowid)
+      };
+    }
+  }, 'query');
 }
 
 /**
@@ -275,7 +277,38 @@ function query(sql, params = []) {
 function transaction(callback) {
   const database = getDb();
   const txn = database.transaction(callback);
-  return txn();
+  return runWithBusyRetry(() => txn(), 'transaction');
+}
+
+function isBusyOrLocked(error) {
+  const message = error instanceof Error ? error.message : String(error);
+  const code = error && error.code ? String(error.code) : '';
+  return code === 'SQLITE_BUSY' || code === 'SQLITE_LOCKED' || /database is locked|database busy/i.test(message);
+}
+
+function sleepSync(ms) {
+  const buffer = new SharedArrayBuffer(4);
+  const view = new Int32Array(buffer);
+  Atomics.wait(view, 0, 0, ms);
+}
+
+function runWithBusyRetry(operation, label) {
+  const maxAttempts = 4;
+  let lastError;
+  for (let attempt = 1; attempt <= maxAttempts; attempt += 1) {
+    try {
+      return operation();
+    } catch (error) {
+      if (!isBusyOrLocked(error) || attempt === maxAttempts) {
+        throw error;
+      }
+      lastError = error;
+      const delayMs = 100 * attempt * attempt;
+      console.warn(`[RA-H MCP] SQLite ${label} hit ${error instanceof Error ? error.message : String(error)}; retrying in ${delayMs}ms (${attempt}/${maxAttempts})`);
+      sleepSync(delayMs);
+    }
+  }
+  throw lastError;
 }
 
 /**
@@ -293,6 +326,7 @@ module.exports = {
   getDb,
   query,
   transaction,
+  runWithBusyRetry,
   closeDatabase,
   getDatabasePath
 };

docs/8_mcp.md

@@ -46,6 +46,15 @@ Important runtime distinction:
 - standalone MCP can read and write nodes/edges without the app running, but it does not own chunking or embedding
 - if standalone MCP writes `nodes.source` while the app is closed, the app later processes that node through startup recovery
 
+## WAL / Multi-Surface Safety
+
+- RA-H uses SQLite WAL as the normal local multi-surface model.
+- The app, standalone MCP, Claude/Codex, and normal reads can coexist.
+- Normal writes should be short; lock collisions wait through SQLite `busy_timeout` plus retry/backoff where supported.
+- Standalone MCP remains first-class and does not require the app to be open.
+- Dangerous maintenance is different from normal reads/writes: restore, DB replacement, checkpoint/truncate, and deleting `rah.sqlite-wal` / `rah.sqlite-shm` require all app/dev/MCP DB owners to be closed first.
+- Use `scripts/database/rah-db-owners.sh "$HOME/Library/Application Support/RA-H/db/rah.sqlite"` before destructive maintenance.
+
 ## Core MCP Contract
 
 - `queryNodes` is the primary tool for direct node retrieval when the user is trying to find a specific existing node.

scripts/database/rah-db-owners.sh

@@ -0,0 +1,30 @@
+#!/usr/bin/env bash
+set -euo pipefail
+
+DB_PATH="${1:-}"
+if [ -z "$DB_PATH" ]; then
+  echo "Usage: $0 <path-to-rah.sqlite>" >&2
+  exit 2
+fi
+
+if ! command -v lsof >/dev/null 2>&1; then
+  echo "lsof is required to inspect live RA-H database owners." >&2
+  exit 3
+fi
+
+paths=("$DB_PATH" "${DB_PATH}-wal" "${DB_PATH}-shm")
+existing=()
+for candidate in "${paths[@]}"; do
+  if [ -e "$candidate" ]; then
+    existing+=("$candidate")
+  fi
+done
+
+if [ "${#existing[@]}" -eq 0 ]; then
+  exit 0
+fi
+
+lsof -FnPc -- "${existing[@]}" 2>/dev/null | awk '
+  /^p/ { pid=substr($0, 2); next }
+  /^c/ { cmd=substr($0, 2); if (pid != "") print pid "\t" cmd }
+' | sort -u

scripts/database/sqlite-backup.sh

@@ -26,6 +26,13 @@ fi
 
 echo "Resolved DB path: $DB_PATH"
 
+OWNERS="$(bash "$(dirname "$0")/rah-db-owners.sh" "$DB_PATH" || true)"
+if [ -n "$OWNERS" ]; then
+  echo "⚠️  Live RA-H DB owners detected while creating a VACUUM INTO backup:"
+  echo "$OWNERS" | sed 's/^/  /'
+  echo "   Continuing because this backup path does not replace/delete DB, WAL, or SHM files."
+fi
+
 BACKUP_DIR="$(dirname "$0")/../backups"
 mkdir -p "$BACKUP_DIR"
 

scripts/database/sqlite-restore.sh

@@ -32,6 +32,14 @@ mkdir -p "$DB_DIR"
 echo "Source backup: $SRC"
 echo "Target DB:     $DB_PATH"
 
+OWNERS="$(bash "$(dirname "$0")/rah-db-owners.sh" "$DB_PATH" || true)"
+if [ -n "$OWNERS" ] && [ "${RAH_ALLOW_LIVE_DB_RESTORE:-}" != "true" ]; then
+  echo "❌ Refusing restore while RA-H DB owners are live:" >&2
+  echo "$OWNERS" | sed 's/^/  /' >&2
+  echo "Close RA-H/MCP/dev processes first, or set RAH_ALLOW_LIVE_DB_RESTORE=true if you have deliberately quiesced them." >&2
+  exit 4
+fi
+
 echo "Verifying backup integrity before restore..."
 ICHECK=$(sqlite3 "$SRC" "PRAGMA integrity_check;")
 echo "  $ICHECK"

scripts/dev/guard-live-db-dev.sh

@@ -0,0 +1,37 @@
+#!/usr/bin/env bash
+set -euo pipefail
+
+ROOT_DIR="$(cd "$(dirname "${BASH_SOURCE[0]}")/../.." && pwd)"
+DEFAULT_DB="$HOME/Library/Application Support/RA-H/db/rah.sqlite"
+
+DB_PATH="${SQLITE_DB_PATH:-}"
+if [ -z "$DB_PATH" ] && [ -f "${ROOT_DIR}/.env.local" ]; then
+  DB_PATH=$(grep -E '^SQLITE_DB_PATH=' "${ROOT_DIR}/.env.local" | sed 's/^SQLITE_DB_PATH=//' | sed 's/^"\(.*\)"$/\1/') || true
+fi
+if [ -z "$DB_PATH" ]; then
+  DB_PATH="$DEFAULT_DB"
+fi
+
+if [ "$DB_PATH" != "$DEFAULT_DB" ]; then
+  exit 0
+fi
+
+echo "⚠️  dev:mac is using the packaged live RA-H DB:"
+echo "   $DB_PATH"
+echo "   Prefer SQLITE_DB_PATH=<dev-db> for isolated development when possible."
+
+owners="$("${ROOT_DIR}/scripts/database/rah-db-owners.sh" "$DB_PATH" || true)"
+if [ -z "$owners" ]; then
+  exit 0
+fi
+
+if [ "${RAH_ALLOW_LIVE_DB_DEV:-}" = "true" ]; then
+  echo "RAH_ALLOW_LIVE_DB_DEV=true set; continuing despite live DB owners:"
+  echo "$owners" | sed 's/^/  /'
+  exit 0
+fi
+
+echo "❌ Refusing to start dev server against the live DB while these processes have it open:"
+echo "$owners" | sed 's/^/  /'
+echo "Close RA-H/MCP owners first, set SQLITE_DB_PATH to a dev DB, or override with RAH_ALLOW_LIVE_DB_DEV=true."
+exit 1

scripts/dev/run-tauri-dev.sh

@@ -9,6 +9,8 @@ NEXT_LOG="${REPO_DIR}/logs/next-dev.log"
 
 mkdir -p "${REPO_DIR}/logs"
 
+"${REPO_DIR}/scripts/dev/guard-live-db-dev.sh"
+
 cleanup() {
   if [[ -n "${NEXT_PID:-}" ]]; then
     echo "Shutting down Next.js dev server (pid ${NEXT_PID})"

src/services/database/sqlite-client.ts

@@ -47,11 +47,13 @@ class SQLiteClient {
   private db: Database.Database;
   private config: SQLiteConfig;
   private readonly readOnly: boolean;
+  private readonly maintenanceMode: boolean;
   private integrityReport: DatabaseIntegrityReport | null = null;
 
   private constructor() {
     this.config = this.getSQLiteConfig();
     this.readOnly = process.env.SQLITE_READONLY === 'true';
+    this.maintenanceMode = process.env.RAH_DB_MAINTENANCE === 'true';
     
     // Initialize database connection
     const dbDirectory = path.dirname(this.config.dbPath);
@@ -84,11 +86,11 @@ class SQLiteClient {
       this.db.pragma('synchronous = NORMAL');
       this.db.pragma('cache_size = 10000');
       this.db.pragma('temp_store = memory');
-      this.db.pragma('busy_timeout = 5000');
+      this.db.pragma('busy_timeout = 10000');
 
       this.withStartupWriteLock(() => {
         this.ensureCoreSchema();
-        // Ensure vector virtual tables are present and healthy
+        // Ensure vector virtual tables are present. Repair/rebuild is maintenance-only.
         this.ensureVectorTables();
         this.healVectorTablesIfCorrupt();
 
@@ -139,26 +141,28 @@ class SQLiteClient {
     params?: any[]
   ): SQLiteQueryResult<T> {
     try {
-      const sqlLower = sql.trim().toLowerCase();
+      return this.runWithBusyRetry(() => {
+        const sqlLower = sql.trim().toLowerCase();
 
-      // Handle different query types
-      if (sqlLower.startsWith('select') || 
-          sqlLower.startsWith('with') ||
-          sqlLower.includes('returning')) {
-        // SELECT queries and queries with RETURNING clause
-        const stmt = this.db.prepare(sql);
-        const rows = params ? stmt.all(...params) : stmt.all();
-        return { rows: rows as T[] };
-      } else {
-        // INSERT/UPDATE/DELETE queries without RETURNING
-        const stmt = this.db.prepare(sql);
-        const result = params ? stmt.run(...params) : stmt.run();
-        return { 
-          rows: [],
-          changes: result.changes,
-          lastInsertRowid: Number(result.lastInsertRowid)
-        };
-      }
+        // Handle different query types
+        if (sqlLower.startsWith('select') ||
+            sqlLower.startsWith('with') ||
+            sqlLower.includes('returning')) {
+          // SELECT queries and queries with RETURNING clause
+          const stmt = this.db.prepare(sql);
+          const rows = params ? stmt.all(...params) : stmt.all();
+          return { rows: rows as T[] };
+        } else {
+          // INSERT/UPDATE/DELETE queries without RETURNING
+          const stmt = this.db.prepare(sql);
+          const result = params ? stmt.run(...params) : stmt.run();
+          return {
+            rows: [],
+            changes: result.changes,
+            lastInsertRowid: Number(result.lastInsertRowid)
+          };
+        }
+      }, 'query');
     } catch (error) {
       this.refreshIntegrityReportForCorruptionError(error);
       console.error('SQLite query error:', error);
@@ -178,17 +182,55 @@ class SQLiteClient {
         details: 'Transactions are not allowed in read-only mode'
       } as DatabaseError;
     }
-    // Proactively validate/repair vec vtables before any write transaction
+    // Proactively validate vec vtables before any write transaction. Destructive
+    // repair/rebuild is only allowed in explicit DB maintenance mode.
     this.healVectorTablesIfCorrupt();
     const txn = this.db.transaction(callback);
     try {
-      return txn();
+      return this.runWithBusyRetry(() => txn(), 'transaction');
     } catch (error) {
       this.refreshIntegrityReportForCorruptionError(error);
       throw this.handleError(error);
     }
   }
 
+  private isBusyOrLocked(error: unknown): boolean {
+    const message = error instanceof Error ? error.message : String(error);
+    const code =
+      typeof error === 'object' &&
+      error !== null &&
+      'code' in error &&
+      typeof (error as { code?: unknown }).code === 'string'
+        ? String((error as { code: string }).code)
+        : '';
+    return code === 'SQLITE_BUSY' || code === 'SQLITE_LOCKED' || /database is locked|database busy/i.test(message);
+  }
+
+  private sleepSync(ms: number): void {
+    const buffer = new SharedArrayBuffer(4);
+    const view = new Int32Array(buffer);
+    Atomics.wait(view, 0, 0, ms);
+  }
+
+  private runWithBusyRetry<T>(operation: () => T, label: string): T {
+    const maxAttempts = 4;
+    let lastError: unknown;
+    for (let attempt = 1; attempt <= maxAttempts; attempt += 1) {
+      try {
+        return operation();
+      } catch (error) {
+        if (!this.isBusyOrLocked(error) || attempt === maxAttempts) {
+          throw error;
+        }
+        lastError = error;
+        const delayMs = 100 * attempt * attempt;
+        console.warn(`[SQLite] ${label} hit ${error instanceof Error ? error.message : String(error)}; retrying in ${delayMs}ms (${attempt}/${maxAttempts})`);
+        this.sleepSync(delayMs);
+      }
+    }
+    throw lastError;
+  }
+
   public async testConnection(): Promise<boolean> {
     try {
       const result = this.query('SELECT datetime() as current_time');
@@ -908,6 +950,12 @@ class SQLiteClient {
         const msg = String(e?.message || '');
         const code = (e && e.code) ? String(e.code) : '';
         if (code === 'SQLITE_CORRUPT_VTAB' || msg.includes('database disk image is malformed') || msg.includes('CORRUPT_VTAB')) {
+          if (!this.maintenanceMode) {
+            console.warn(
+              `Detected corrupted virtual table ${table}, but repair is disabled outside RAH_DB_MAINTENANCE=true. Use explicit maintenance/rebuild flow.`
+            );
+            return;
+          }
           console.warn(`Detected corrupted virtual table ${table} (${code || 'error'}). Recreating...`);
           try {
             this.db.exec(`DROP TABLE IF EXISTS ${table};`);