Fix agent close persistence, whitespace diff filtering, and diff param cleanup

- Persist snapshot before emitting closed agent to avoid data loss
- Flush after branch rename so state hits disk immediately
- Filter phantom whitespace-only files from ignore-whitespace diffs
- Only include ignoreWhitespace param when true to keep payloads clean
- Add createFeature test helper for AgentFeature construction

packages/server/src/client/daemon-client.ts

@@ -2226,15 +2226,20 @@ export class DaemonClient {
     baseRef?: string;
     ignoreWhitespace?: boolean;
   }): { mode: "uncommitted" | "base"; baseRef?: string; ignoreWhitespace?: boolean } {
-    const ignoreWhitespace = compare.ignoreWhitespace === true;
     if (compare.mode === "uncommitted") {
-      return { mode: "uncommitted", ignoreWhitespace };
+      return compare.ignoreWhitespace === true
+        ? { mode: "uncommitted", ignoreWhitespace: true }
+        : { mode: "uncommitted" };
     }
     const trimmedBaseRef = compare.baseRef?.trim();
     if (!trimmedBaseRef) {
-      return { mode: "base", ignoreWhitespace };
+      return compare.ignoreWhitespace === true
+        ? { mode: "base", ignoreWhitespace: true }
+        : { mode: "base" };
     }
-    return { mode: "base", baseRef: trimmedBaseRef, ignoreWhitespace };
+    return compare.ignoreWhitespace === true
+      ? { mode: "base", baseRef: trimmedBaseRef, ignoreWhitespace: true }
+      : { mode: "base", baseRef: trimmedBaseRef };
   }
 
   async getCheckoutDiff(

packages/server/src/server/agent/agent-manager.test.ts

@@ -13,6 +13,7 @@ import { AgentManager } from "./agent-manager.js";
 import { AgentStorage } from "./agent-storage.js";
 import type {
   AgentClient,
+  AgentFeature,
   AgentLaunchContext,
   AgentPersistenceHandle,
   AgentRunResult,
@@ -47,6 +48,15 @@ const TEST_CAPABILITIES = {
   supportsToolInvocations: false,
 } as const;
 
+function createFeature(args: { id: string; label: string; value: boolean }): AgentFeature {
+  return {
+    type: "toggle",
+    id: args.id,
+    label: args.label,
+    value: args.value,
+  };
+}
+
 async function seedWorkspace(
   database: PaseoDatabaseHandle,
   options: { directory: string },

packages/server/src/server/agent/agent-manager.ts

@@ -725,7 +725,8 @@ export class AgentManager {
     const closedAgent = this.prepareAgentForClosure(agent, "agent closed");
     await agent.session.close();
     this.timelineStore.delete(agentId);
-    this.emitClosedAgent(closedAgent);
+    await this.persistSnapshot(closedAgent);
+    this.emitClosedAgent(closedAgent, { persist: false });
     this.logger.trace({ agentId }, "closeAgent: completed");
   }
 
@@ -1944,8 +1945,8 @@ export class AgentManager {
     };
   }
 
-  private emitClosedAgent(agent: ManagedAgentClosed): void {
-    this.emitState(agent);
+  private emitClosedAgent(agent: ManagedAgentClosed, options?: { persist?: boolean }): void {
+    this.emitState(agent, options);
   }
   private subscribeToSession(agent: ActiveManagedAgent): void {
     if (agent.unsubscribeSession) {

packages/server/src/server/agent/agent-metadata-generator.ts

@@ -233,6 +233,7 @@ export async function generateAndApplyAgentMetadata(
     try {
       await renameCurrentBranchImpl(options.cwd, normalizedBranch);
       options.agentManager.notifyAgentState(options.agentId);
+      await options.agentManager.flush();
     } catch (error) {
       options.logger.warn(
         { err: error, agentId: options.agentId, branch: normalizedBranch },

packages/server/src/utils/checkout-git.ts

@@ -1547,6 +1547,16 @@ export async function getCheckoutDiff(
         continue;
       }
 
+      // `git diff -w --name-status` can still surface paths whose only changes were
+      // whitespace. Skip those empty tracked entries so callers don't see phantom files.
+      if (
+        ignoreWhitespace &&
+        change.status.startsWith("M") &&
+        (!stat || (!stat.isBinary && stat.additions === 0 && stat.deletions === 0))
+      ) {
+        continue;
+      }
+
       structured.push({
         path: change.path,
         isNew: change.isNew,