fix(migration): prevent compat-renamed version slot from shadowing new migrations (#1637)

After reconcileRenumberedMigrations() rewrites a legacy row (e.g. 028→029),
verify the old version slot is clear. A residual row at the old version
would cause getAppliedVersions() to skip the new migration file at that
version number (028_create_files_and_batches.sql).

Also adds 'batches' table to PHYSICAL_SCHEMA_SENTINELS for physical
schema recovery on upgrade paths.

CHANGELOG.md

@@ -27,6 +27,7 @@
 - **fix(types):** Add explicit type annotations to sync-env test helpers and dynamic import casts to satisfy `typecheck:noimplicit:core` CI gate.
 - **fix(reasoning):** Implement Reasoning Replay Cache — hybrid memory/SQLite persistence for `reasoning_content` in multi-turn tool-calling flows. Automatically captures reasoning from DeepSeek V4, Kimi K2, Qwen-Thinking, and GLM models and re-injects it on follow-up turns to prevent HTTP 400 errors from strict reasoning-content validation. Includes dashboard telemetry tab, REST API, and 21 unit tests (#1628 — thanks @JasonLandbridge).
 - **fix(postinstall):** Extend postinstall native module repair to cover `wreq-js` — detects missing platform-specific `.node` binaries inside `app/node_modules/wreq-js/rust/` and copies them from the root install. Fixes global `pnpm` installs on macOS arm64 where the standalone app directory only contained Linux binaries (#1634 — thanks @MarcosT96).
+- **fix(migration):** Prevent compat-renamed migration slots from shadowing new migrations at the same version number. After rewriting `028_provider_connection_max_concurrent` → `029`, the runner now verifies the old version slot is clear, ensuring `028_create_files_and_batches` runs on v3.6.x → v3.7.x upgrades. Adds `batches` table as a physical schema sentinel for upgrade recovery (#1637 — thanks @V8-Software).
 
 ### 📝 Documentation
 

src/lib/db/migrationRunner.ts

@@ -74,6 +74,7 @@ const RENAMED_MIGRATION_COMPATIBILITY = [
 ] as const;
 
 const PHYSICAL_SCHEMA_SENTINELS = [
+  { version: "028", tableName: "batches", description: "batches table" },
   { version: "024", tableName: "sync_tokens", description: "sync_tokens table" },
   { version: "022", tableName: "memory_fts", description: "memory_fts virtual table" },
   { version: "019", tableName: "context_handoffs", description: "context_handoffs table" },
@@ -268,6 +269,25 @@ function reconcileRenumberedMigrations(
       `[Migration] Reconciled renamed migration ${compatibility.fromVersion}_${compatibility.fromName} ` +
         `to ${compatibility.toVersion}_${compatibility.toName} to preserve pending migrations.`
     );
+
+    // After the compat rewrite, verify the old version slot is now free.
+    // A residual row (from a failed prior run, manual intervention, or edge-case
+    // UPDATE conflict) at the old version would shadow a NEW migration file
+    // placed at that version number — e.g. 028_create_files_and_batches.sql
+    // would be skipped because getAppliedVersions() still sees version "028".
+    const residualRow = db
+      .prepare("SELECT version, name FROM _omniroute_migrations WHERE version = ?")
+      .get(compatibility.fromVersion) as { version: string; name: string } | undefined;
+    if (residualRow) {
+      console.warn(
+        `[Migration] ⚠️  Residual row at version ${compatibility.fromVersion} ` +
+          `(name: "${residualRow.name}") still present after compat rewrite — ` +
+          `removing to unblock new migration at this version slot.`
+      );
+      db.prepare("DELETE FROM _omniroute_migrations WHERE version = ?").run(
+        compatibility.fromVersion
+      );
+    }
   }
 
   return repaired;