Fix sidebar project removal

Remove projects through a daemon RPC so the sidebar can delete the project
record after archiving its active workspaces. Reopening a removed directory
recreates the missing project record so local projects keep their derived
basename, and History skips orphaned archived workspace rows.

Fixes #1583.

packages/app/src/stores/session-store.test.ts

@@ -48,6 +48,7 @@ function getTestSessionReferences() {
     sessions: state.sessions,
     session,
     workspaces: session.workspaces,
+    emptyProjects: session.emptyProjects,
   };
 }
 
@@ -448,6 +449,48 @@ describe("removeWorkspace", () => {
   });
 });
 
+describe("removeEmptyProject", () => {
+  it("removes an empty project by project id", () => {
+    const store = useSessionStore.getState();
+    initializeTestSession();
+    store.setEmptyProjects("test-server", [
+      {
+        projectId: "project-empty",
+        projectDisplayName: "Empty",
+        projectCustomName: null,
+        projectRootPath: "/repo/empty",
+        projectKind: "git",
+      },
+    ]);
+
+    store.removeEmptyProject("test-server", "project-empty");
+
+    expect(getTestSessionReferences().emptyProjects.has("project-empty")).toBe(false);
+  });
+
+  it("preserves identity when removing a missing empty project", () => {
+    const store = useSessionStore.getState();
+    initializeTestSession();
+    store.setEmptyProjects("test-server", [
+      {
+        projectId: "project-empty",
+        projectDisplayName: "Empty",
+        projectCustomName: null,
+        projectRootPath: "/repo/empty",
+        projectKind: "git",
+      },
+    ]);
+    const before = getTestSessionReferences();
+
+    store.removeEmptyProject("test-server", "project-missing");
+    const after = getTestSessionReferences();
+
+    expect(after.sessions).toBe(before.sessions);
+    expect(after.session).toBe(before.session);
+    expect(after.emptyProjects).toBe(before.emptyProjects);
+  });
+});
+
 describe("patchWorkspaceScripts", () => {
   it("preserves workspace entry identity when scripts are content-equal", () => {
     const script = {

packages/app/src/stores/session-store.ts

@@ -460,6 +460,7 @@ interface SessionStoreActions {
   removeWorkspace: (serverId: string, workspaceId: string) => void;
   setEmptyProjects: (serverId: string, emptyProjects: Iterable<EmptyProjectDescriptor>) => void;
   addEmptyProject: (serverId: string, emptyProject: EmptyProjectDescriptor) => void;
+  removeEmptyProject: (serverId: string, projectId: string) => void;
   setWorkspaceRestoreStatus: (
     serverId: string,
     workspaceId: string,
@@ -1265,6 +1266,24 @@ export const useSessionStore = create<SessionStore>()(
         });
       },
 
+      removeEmptyProject: (serverId, projectId) => {
+        set((prev) => {
+          const session = prev.sessions[serverId];
+          if (!session?.emptyProjects.has(projectId)) {
+            return prev;
+          }
+          const next = new Map(session.emptyProjects);
+          next.delete(projectId);
+          return {
+            ...prev,
+            sessions: {
+              ...prev.sessions,
+              [serverId]: { ...session, emptyProjects: next },
+            },
+          };
+        });
+      },
+
       setWorkspaceRestoreStatus: (serverId, workspaceId, status) => {
         set((prev) => {
           const session = prev.sessions[serverId];