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();
   }