diff --git a/apps/server/src/cli/thread.ts b/apps/server/src/cli/thread.ts
index ff27441dc089..53b42063b5df 100644
--- a/apps/server/src/cli/thread.ts
+++ b/apps/server/src/cli/thread.ts
@@ -69,6 +69,9 @@ export class ThreadCliError extends Schema.TaggedErrorClass<ThreadCliError>()("T
 const encodeJson = Schema.encodeEffect(Schema.fromJsonString(Schema.Unknown));
 const isThreadCliError = Schema.is(ThreadCliError);
 
+const currentThreadIdForHome = (home: string): string | undefined =>
+  process.env.T3CODE_HOME?.trim() === home ? process.env.T3CODE_THREAD_ID?.trim() : undefined;
+
 const ThreadIdentity = Schema.Struct({
   environmentId: Schema.String,
   threadId: Schema.String,
@@ -890,6 +893,7 @@ const runThreadSend = Effect.fn("runThreadSend")(function* (
     Effect.mapError((cause) => new ThreadSendServerUnavailableError({ cause })),
   );
   const minimumLogLevel = config.logLevel;
+  const currentThreadId = currentThreadIdForHome(config.baseDir);
 
   return yield* Effect.gen(function* () {
     const auth = yield* EnvironmentAuth.EnvironmentAuth;
@@ -956,12 +960,10 @@ const runThreadSend = Effect.fn("runThreadSend")(function* (
               commandId,
               messageId,
               createdAt: DateTime.formatIso(yield* DateTime.now),
-              ...(process.env.T3CODE_THREAD_ID?.trim()
-                ? { sourceThreadId: ThreadId.make(process.env.T3CODE_THREAD_ID.trim()) }
-                : {}),
+              ...(currentThreadId ? { sourceThreadId: ThreadId.make(currentThreadId) } : {}),
               ...(waitForCompletion ? { trackRequestCorrelation: true as const } : {}),
-              ...(waitForCompletion && process.env.T3CODE_THREAD_ID?.trim()
-                ? { rejectWaitForThreadId: ThreadId.make(process.env.T3CODE_THREAD_ID.trim()) }
+              ...(waitForCompletion && currentThreadId
+                ? { rejectWaitForThreadId: ThreadId.make(currentThreadId) }
                 : {}),
             },
           );
@@ -1046,7 +1048,7 @@ const runThreadWait = Effect.fn("runThreadWait")(function* (
       ),
     });
   }
-  const currentThreadId = process.env.T3CODE_THREAD_ID?.trim();
+  const currentThreadId = currentThreadIdForHome(config.baseDir);
   const waitingOnCurrentThread = currentThreadId === waitHandle.threadId;
   return yield* Effect.gen(function* () {
     const auth = yield* EnvironmentAuth.EnvironmentAuth;
diff --git a/apps/server/src/persistence/Migrations/016_CanonicalizeModelSelections.test.ts b/apps/server/src/persistence/Migrations/016_CanonicalizeModelSelections.test.ts
index 451351496880..fff5a738622d 100644
--- a/apps/server/src/persistence/Migrations/016_CanonicalizeModelSelections.test.ts
+++ b/apps/server/src/persistence/Migrations/016_CanonicalizeModelSelections.test.ts
@@ -381,11 +381,11 @@ layer("016_CanonicalizeModelSelections", (it) => {
   );
 });
 
-layer("053_ClearAutomaticProjectModelDefaults", (it) => {
+layer("044_ClearAutomaticProjectModelDefaults", (it) => {
   it.effect("clears create-time seeds and preserves explicit project defaults", () =>
     Effect.gen(function* () {
       const sql = yield* SqlClient.SqlClient;
-      yield* runMigrations({ toMigrationInclusive: 52 });
+      yield* runMigrations({ toMigrationInclusive: 43 });
 
       yield* sql`
         INSERT INTO projection_projects (
@@ -429,7 +429,7 @@ layer("053_ClearAutomaticProjectModelDefaults", (it) => {
           ('event-explicit-update', 'project', 'project-explicit', 1, 'project.meta-updated', '2026-08-02T00:00:00.000Z', 'command-explicit-update', NULL, 'command-explicit-update', 'client', '{"defaultModelSelection":{"instanceId":"codex","model":"gpt-5.6-sol","options":[{"id":"reasoningEffort","value":"high"}]}}', '{}')
       `;
 
-      yield* runMigrations({ toMigrationInclusive: 53 });
+      yield* runMigrations({ toMigrationInclusive: 44 });
 
       const projects = yield* sql<{
         readonly projectId: string;
diff --git a/apps/server/src/persistence/Migrations/046_RepairAutomaticSettlementTimestamps.test.ts b/apps/server/src/persistence/Migrations/046_RepairAutomaticSettlementTimestamps.test.ts
index 069799502507..f562fa655a11 100644
--- a/apps/server/src/persistence/Migrations/046_RepairAutomaticSettlementTimestamps.test.ts
+++ b/apps/server/src/persistence/Migrations/046_RepairAutomaticSettlementTimestamps.test.ts
@@ -10,11 +10,11 @@ const layer = it.layer(Layer.mergeAll(NodeSqliteClient.layerMemory()));
 
 const MODEL_SELECTION = '{"instanceId":"codex","model":"gpt-5.6-sol"}';
 
-layer("055_RepairAutomaticSettlementTimestamps", (it) => {
+layer("046_RepairAutomaticSettlementTimestamps", (it) => {
   it.effect("repairs automatic stamps and leaves manual settlement alone", () =>
     Effect.gen(function* () {
       const sql = yield* SqlClient.SqlClient;
-      yield* runMigrations({ toMigrationInclusive: 54 });
+      yield* runMigrations({ toMigrationInclusive: 45 });
 
       yield* sql`
         INSERT INTO projection_threads (
@@ -164,7 +164,7 @@ layer("055_RepairAutomaticSettlementTimestamps", (it) => {
       const eventsBefore =
         yield* sql`SELECT payload_json FROM orchestration_events ORDER BY event_id`;
 
-      yield* runMigrations({ toMigrationInclusive: 55 });
+      yield* runMigrations({ toMigrationInclusive: 46 });
 
       const threads = yield* sql<{
         readonly threadId: string;
diff --git a/apps/server/src/provider/Layers/CursorProvider.test.ts b/apps/server/src/provider/Layers/CursorProvider.test.ts
index 98983b4b4434..ac9837d43ebd 100644
--- a/apps/server/src/provider/Layers/CursorProvider.test.ts
+++ b/apps/server/src/provider/Layers/CursorProvider.test.ts
@@ -368,18 +368,19 @@ describe("Cursor skills", () => {
           "not a directory",
         );
 
+        const realWorkspace = yield* fileSystem.realPath(workspace);
         const skills = yield* discoverCursorSkills(workspace, { HOME: userHome });
         expect(skills).toEqual([
           {
             name: "internal",
-            path: path.join(workspace, ".cursor", "skills", "internal", "SKILL.md"),
+            path: path.join(realWorkspace, ".cursor", "skills", "internal", "SKILL.md"),
             scope: "project",
             enabled: true,
             userInvocable: false,
           },
           {
             name: "oversized",
-            path: path.join(workspace, ".cursor", "skills", "oversized", "SKILL.md"),
+            path: path.join(realWorkspace, ".cursor", "skills", "oversized", "SKILL.md"),
             scope: "project",
             enabled: true,
           },
@@ -387,7 +388,7 @@ describe("Cursor skills", () => {
             name: "review",
             displayName: "Review changes",
             description: "project review",
-            path: path.join(workspace, ".agents", "skills", "nested", "review", "SKILL.md"),
+            path: path.join(realWorkspace, ".agents", "skills", "nested", "review", "SKILL.md"),
             scope: "project",
             enabled: true,
           },
diff --git a/scripts/lastcode-local-update.mjs b/scripts/lastcode-local-update.mjs
index c490d87ee68d..e10ef5c78e4d 100644
--- a/scripts/lastcode-local-update.mjs
+++ b/scripts/lastcode-local-update.mjs
@@ -688,7 +688,9 @@ function buildUnlocked(options, updateRoot) {
     if (!NodeFS.existsSync(installer)) {
       throw new Error(`Checkpoint automation dependencies are missing at ${installer}.`);
     }
-    run(worktreePath, installer, ["install", "--frozen-lockfile"], { logFd });
+    // The retained build worktree can otherwise keep stale snapshots of local
+    // file dependencies when their source changes without a lockfile change.
+    run(worktreePath, installer, ["install", "--frozen-lockfile", "--force"], { logFd });
     const mise = resolveMise(options.home);
     const nodeCommand = ["exec", "node@24.13.1", "--", "node"];
     const nodeExecutable = run(worktreePath, mise, [...nodeCommand, "-p", "process.execPath"]);