fix: prevent SQLite corruption by checkpointing WAL and closing DB on shutdown

The database was never properly closed on SIGINT/SIGTERM — WAL files were left
in a partially-written state causing "database disk image is malformed" errors.
Adds WAL checkpoint on close, synchronous=NORMAL pragma, SIGTERM handlers, and
a store.close() method that flushes all pending writes before exit.

Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>

packages/core/src/central-db.ts

@@ -122,6 +122,8 @@ export class CentralDatabase {
 
     // Enable WAL mode for concurrent reader/writer access
     this.db.exec("PRAGMA journal_mode = WAL");
+    // Ensure data reaches disk on commit (NORMAL is safe with WAL mode)
+    this.db.exec("PRAGMA synchronous = NORMAL");
     // Enable foreign key enforcement
     this.db.exec("PRAGMA foreign_keys = ON");
   }
@@ -144,8 +146,14 @@ export class CentralDatabase {
 
   /**
    * Close the database connection.
+   * Checkpoints the WAL first to ensure all writes are flushed to the main db file.
    */
   close(): void {
+    try {
+      this.db.exec("PRAGMA wal_checkpoint(TRUNCATE)");
+    } catch {
+      // Best-effort: checkpoint failure is non-fatal
+    }
     this.db.close();
   }
 

packages/core/src/db.ts

@@ -264,6 +264,8 @@ export class Database {
 
     // Enable WAL mode for concurrent reader/writer access
     this.db.exec("PRAGMA journal_mode = WAL");
+    // Ensure data reaches disk on commit (NORMAL is safe with WAL mode)
+    this.db.exec("PRAGMA synchronous = NORMAL");
     // Enable foreign key enforcement
     this.db.exec("PRAGMA foreign_keys = ON");
   }
@@ -368,10 +370,25 @@ export class Database {
     }
   }
 
+  /**
+   * Checkpoint the WAL file back into the main database.
+   * This reduces the risk of corruption from incomplete WAL writes
+   * and keeps the WAL file from growing unbounded.
+   */
+  checkpoint(): void {
+    try {
+      this.db.exec("PRAGMA wal_checkpoint(TRUNCATE)");
+    } catch {
+      // Best-effort: checkpoint failure is non-fatal
+    }
+  }
+
   /**
    * Close the database connection.
+   * Checkpoints the WAL first to ensure all writes are flushed to the main db file.
    */
   close(): void {
+    this.checkpoint();
     this.db.close();
   }
 

packages/core/src/store.ts

@@ -1693,6 +1693,18 @@ export class TaskStore extends EventEmitter<TaskStoreEvents> {
     this.recentlyWritten.clear();
   }
 
+  /**
+   * Gracefully shut down: stop watching and close the database connection.
+   * Ensures WAL is checkpointed so no pending writes are lost.
+   */
+  close(): void {
+    this.stopWatching();
+    if (this._db) {
+      this._db.close();
+      this._db = null;
+    }
+  }
+
   /**
    * Mark a file path as recently written by an in-process mutation
    * so the watcher will skip it.