Wait for SQLite locks instead of crashing

A second process (rebuild, ghidra refresh) holding a write lock made the
verifier's timer throw "database is locked" and took the coordinator down.
Set a busy timeout and keep timer errors from killing the process.

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01RNwtXPYqFu3oKaaXwYwNWW

src/server/app.js

@@ -631,7 +631,7 @@ export async function startServer(dataDir) {
   ctx.tasks.generate();
   ctx.verifier.start();
   ctx.merger.start();
-  const sweeper = setInterval(() => ctx.tasks.sweepExpired(), 60_000);
+  const sweeper = setInterval(() => { try { ctx.tasks.sweepExpired(); } catch (e) { console.error(`lease sweep: ${e.message}`); } }, 60_000);
   const server = createApp(ctx);
   await new Promise((r) => server.listen(ctx.config.listen.port, ctx.config.listen.host, r));
   console.log(`clank together coordinator listening on http://${ctx.config.listen.host}:${ctx.config.listen.port} (public url ${ctx.config.publicUrl})`);

src/server/db.js

@@ -214,6 +214,8 @@ export const hashToken = (t) => crypto.createHash('sha256').update(t).digest('he
 export class Store {
   constructor(file) {
     this.db = new DatabaseSync(file);
+    // CLI commands (rebuild, ghidra refresh) write from a second process; wait for their locks.
+    this.db.exec('PRAGMA busy_timeout = 15000');
     this.migrateUsers();
     this.db.exec(SCHEMA);
     this.addColumn('func_status', 'confirmed', 'INTEGER NOT NULL DEFAULT 0');

src/server/merge.js

@@ -15,7 +15,7 @@ export class Merger {
   start() {
     this.store.run(`UPDATE batches SET state = 'open' WHERE state = 'merging'`);
     this.store.run(`UPDATE tasks SET state = 'approved' WHERE state = 'merging'`);
-    this.timer = setInterval(() => this.pump(), 3000);
+    this.timer = setInterval(() => { try { this.pump(); } catch (e) { console.error(`merge pump: ${e.message}`); } }, 3000);
   }
 
   stop() {

src/server/verify.js

@@ -38,7 +38,7 @@ export class Verifier {
       );
       this.store.run('UPDATE attempts SET batch_id = ? WHERE id = ?', Number(b.lastInsertRowid), a.id);
     }
-    this.timer = setInterval(() => this.pump(), 2000);
+    this.timer = setInterval(() => { try { this.pump(); } catch (e) { console.error(`verify pump: ${e.message}`); } }, 2000);
     this.pump();
   }