fix(core): soft-delete source connections with deleted_at

Migration 0003 adds source_connections.deleted_at. deleteConnection sets it; listing, lookups,
updates, the scheduler and the sync handler ignore deleted connections, so a paused
credential-less connection stays visible and can be resumed.

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>

packages/core/test/connections.test.ts

@@ -55,7 +55,8 @@ forEachDialect("connections", (getDb) => {
     r = await raw(id);
     expect(r.status).toBe("paused");
     expect(r.credentials_enc).toBeNull();
-    expect((await listConnections(db, u))[0]!.hasCredentials).toBe(false);
+    expect(r.deleted_at).not.toBeNull();
+    expect(await listConnections(db, u)).toEqual([]);
   });
 
   test("cursor persists on set; http uses manifest rate limit", async () => {