fix(agent-core-v2): dedupe workspace registry entries by root

Port v1 #1221: collapse registered workspaces that share a root in list(), preferring the entry whose id matches the current canonical encodeWorkDirKey, so a legacy workspaces.json (v1-compatible) does not render the same folder twice through GET /workspaces.

packages/agent-core-v2/src/app/workspaceRegistry/workspaceRegistryService.ts

@@ -49,7 +49,7 @@ export class WorkspaceRegistryService implements IWorkspaceRegistry {
   list(): Promise<readonly Workspace[]> {
     return this.runExclusive(async () => {
       const cache = await this.ensureLoaded();
-      return [...cache.values()];
+      return dedupeByRoot(cache);
     });
   }
 
@@ -174,6 +174,30 @@ function parseSessionIndexLine(line: string): SessionIndexLine | undefined {
   }
 }
 
+/**
+ * Collapse registered workspaces that share a `root`. The persisted catalog
+ * (v1-compatible `workspaces.json`) can hold legacy entries whose id was
+ * computed by an older `encodeWorkDirKey` (e.g. realpath-based on Windows) for
+ * the same folder, so one root may map to multiple ids. Prefer the entry whose
+ * id matches the current canonical key so current sessions' `workspace_id`
+ * still resolves and the same folder is not listed twice.
+ */
+function dedupeByRoot(cache: ReadonlyMap<string, Workspace>): Workspace[] {
+  const byRoot = new Map<string, Workspace>();
+  for (const ws of cache.values()) {
+    const existing = byRoot.get(ws.root);
+    if (existing === undefined) {
+      byRoot.set(ws.root, ws);
+      continue;
+    }
+    const canonicalId = encodeWorkDirKey(ws.root);
+    if (existing.id !== canonicalId && ws.id === canonicalId) {
+      byRoot.set(ws.root, ws);
+    }
+  }
+  return [...byRoot.values()];
+}
+
 registerScopedService(
   LifecycleScope.App,
   IWorkspaceRegistry,

packages/agent-core-v2/test/workspaceRegistry/workspaceRegistryService.test.ts

@@ -167,4 +167,28 @@ describe('WorkspaceRegistryService (file-backed)', () => {
     await build().delete(created.id);
     expect(await restart().get(created.id)).toBeUndefined();
   });
+
+  it('collapses duplicate registered entries for the same root, preferring the canonical id', async () => {
+    const root = join(homeDir, 'dup');
+    const canonicalId = encodeWorkDirKey(root);
+    // Simulate a registry that also holds a legacy id for the same folder (e.g.
+    // one produced by an older encodeWorkDirKey).
+    const legacyId = 'wd_duplegacy_deadbeef0000';
+    const entry: PersistedWorkspaceEntry = {
+      root,
+      name: 'dup',
+      created_at: '2026-01-01T00:00:00.000Z',
+      last_opened_at: '2026-01-01T00:00:00.000Z',
+    };
+    await writeWorkspacesJson({
+      // Legacy first so the canonical entry must actively replace it.
+      [legacyId]: entry,
+      [canonicalId]: entry,
+    });
+
+    const list = await build().list();
+    const matches = list.filter((w) => w.root === root);
+    expect(matches).toHaveLength(1);
+    expect(matches[0]?.id).toBe(canonicalId);
+  });
 });