[codex] Improve workspace runtime and navigation ergonomics (#3680)

## Thinking Path

> - Paperclip orchestrates AI agents for zero-human companies
> - That operator experience depends not just on issue chat, but also on
how workspaces, inbox groups, and navigation state behave over
long-running sessions
> - The current branch included a separate cluster of workspace-runtime
controls, inbox grouping, sidebar ordering, and worktree lifecycle fixes
> - Those changes cross server, shared contracts, database state, and UI
navigation, but they still form one coherent operator workflow area
> - This pull request isolates the workspace/runtime and navigation
ergonomics work into one standalone branch
> - The benefit is better workspace recovery and navigation persistence
without forcing reviewers through the unrelated issue-detail/chat work

## What Changed

- Improved execution workspace and project workspace controls, request
wiring, layout, and JSON editor ergonomics
- Hardened linked worktree reuse/startup behavior and documented the
`worktree repair` flow for recovering linked worktrees safely
- Added inbox workspace grouping, mobile collapse, archive undo,
keyboard navigation, shared group-header styling, and persisted
collapsed-group behavior
- Added persistent sidebar order preferences with the supporting DB
migration, shared/server contracts, routes, services, hooks, and UI
integration
- Scoped issue-list preferences by context and added targeted UI/server
tests for workspace controls, inbox behavior, sidebar preferences, and
worktree validation

## Verification

- `pnpm vitest run
server/src/__tests__/sidebar-preferences-routes.test.ts
ui/src/pages/Inbox.test.tsx
ui/src/components/ProjectWorkspaceSummaryCard.test.tsx
ui/src/components/WorkspaceRuntimeControls.test.tsx
ui/src/api/workspace-runtime-control.test.ts`
- `server/src/__tests__/workspace-runtime.test.ts` was attempted, but
the embedded Postgres suite self-skipped/hung on this host after
reporting an init-script issue, so it is not counted as a local pass
here

## Risks

- Medium: this branch includes migration-backed preference storage plus
worktree/runtime behavior, so merge review should pay attention to state
persistence and worktree recovery semantics
- The sidebar preference migration is standalone, but it should still be
watched for conflicts if another migration lands first

## Model Used

- OpenAI Codex coding agent (GPT-5-class runtime in Codex CLI; exact
deployed model ID is not exposed in this environment), reasoning
enabled, tool use and local code execution enabled

## Checklist

- [x] I have included a thinking path that traces from project context
to this change
- [x] I have specified the model used (with version and capability
details)
- [ ] I have run tests locally and they pass
- [x] I have added or updated tests where applicable
- [ ] If this change affects the UI, I have included before/after
screenshots
- [x] I have updated relevant documentation to reflect my changes
- [x] I have considered and documented any risks above
- [x] I will address all Greptile and reviewer comments before
requesting merge

---------

Co-authored-by: Paperclip <noreply@paperclip.ing>

ui/src/api/execution-workspaces.ts

@@ -1,5 +1,11 @@
-import type { ExecutionWorkspace, ExecutionWorkspaceCloseReadiness, WorkspaceOperation } from "@paperclipai/shared";
+import type {
+  ExecutionWorkspace,
+  ExecutionWorkspaceCloseReadiness,
+  WorkspaceOperation,
+  WorkspaceRuntimeControlTarget,
+} from "@paperclipai/shared";
 import { api } from "./client";
+import { sanitizeWorkspaceRuntimeControlTarget } from "./workspace-runtime-control";
 
 export const executionWorkspacesApi = {
   list: (
@@ -26,10 +32,23 @@ export const executionWorkspacesApi = {
     api.get<ExecutionWorkspaceCloseReadiness>(`/execution-workspaces/${id}/close-readiness`),
   listWorkspaceOperations: (id: string) =>
     api.get<WorkspaceOperation[]>(`/execution-workspaces/${id}/workspace-operations`),
-  controlRuntimeServices: (id: string, action: "start" | "stop" | "restart") =>
+  controlRuntimeServices: (
+    id: string,
+    action: "start" | "stop" | "restart",
+    target: WorkspaceRuntimeControlTarget = {},
+  ) =>
     api.post<{ workspace: ExecutionWorkspace; operation: WorkspaceOperation }>(
       `/execution-workspaces/${id}/runtime-services/${action}`,
-      {},
+      sanitizeWorkspaceRuntimeControlTarget(target),
+    ),
+  controlRuntimeCommands: (
+    id: string,
+    action: "start" | "stop" | "restart" | "run",
+    target: WorkspaceRuntimeControlTarget = {},
+  ) =>
+    api.post<{ workspace: ExecutionWorkspace; operation: WorkspaceOperation }>(
+      `/execution-workspaces/${id}/runtime-commands/${action}`,
+      sanitizeWorkspaceRuntimeControlTarget(target),
     ),
   update: (id: string, data: Record<string, unknown>) => api.patch<ExecutionWorkspace>(`/execution-workspaces/${id}`, data),
 };

ui/src/api/index.ts

@@ -15,5 +15,6 @@ export { dashboardApi } from "./dashboard";
 export { heartbeatsApi } from "./heartbeats";
 export { instanceSettingsApi } from "./instanceSettings";
 export { sidebarBadgesApi } from "./sidebarBadges";
+export { sidebarPreferencesApi } from "./sidebarPreferences";
 export { inboxDismissalsApi } from "./inboxDismissals";
 export { companySkillsApi } from "./companySkills";

ui/src/api/projects.ts

@@ -1,5 +1,11 @@
-import type { Project, ProjectWorkspace, WorkspaceOperation } from "@paperclipai/shared";
+import type {
+  Project,
+  ProjectWorkspace,
+  WorkspaceOperation,
+  WorkspaceRuntimeControlTarget,
+} from "@paperclipai/shared";
 import { api } from "./client";
+import { sanitizeWorkspaceRuntimeControlTarget } from "./workspace-runtime-control";
 
 function withCompanyScope(path: string, companyId?: string) {
   if (!companyId) return path;
@@ -32,10 +38,22 @@ export const projectsApi = {
     workspaceId: string,
     action: "start" | "stop" | "restart",
     companyId?: string,
+    target: WorkspaceRuntimeControlTarget = {},
   ) =>
     api.post<{ workspace: ProjectWorkspace; operation: WorkspaceOperation }>(
       projectPath(projectId, companyId, `/workspaces/${encodeURIComponent(workspaceId)}/runtime-services/${action}`),
-      {},
+      sanitizeWorkspaceRuntimeControlTarget(target),
+    ),
+  controlWorkspaceCommands: (
+    projectId: string,
+    workspaceId: string,
+    action: "start" | "stop" | "restart" | "run",
+    companyId?: string,
+    target: WorkspaceRuntimeControlTarget = {},
+  ) =>
+    api.post<{ workspace: ProjectWorkspace; operation: WorkspaceOperation }>(
+      projectPath(projectId, companyId, `/workspaces/${encodeURIComponent(workspaceId)}/runtime-commands/${action}`),
+      sanitizeWorkspaceRuntimeControlTarget(target),
     ),
   removeWorkspace: (projectId: string, workspaceId: string, companyId?: string) =>
     api.delete<ProjectWorkspace>(projectPath(projectId, companyId, `/workspaces/${encodeURIComponent(workspaceId)}`)),

ui/src/api/sidebarPreferences.ts

@@ -0,0 +1,12 @@
+import type { SidebarOrderPreference, UpsertSidebarOrderPreference } from "@paperclipai/shared";
+import { api } from "./client";
+
+export const sidebarPreferencesApi = {
+  getCompanyOrder: () => api.get<SidebarOrderPreference>("/sidebar-preferences/me"),
+  updateCompanyOrder: (data: UpsertSidebarOrderPreference) =>
+    api.put<SidebarOrderPreference>("/sidebar-preferences/me", data),
+  getProjectOrder: (companyId: string) =>
+    api.get<SidebarOrderPreference>(`/companies/${companyId}/sidebar-preferences/me`),
+  updateProjectOrder: (companyId: string, data: UpsertSidebarOrderPreference) =>
+    api.put<SidebarOrderPreference>(`/companies/${companyId}/sidebar-preferences/me`, data),
+};

ui/src/api/workspace-runtime-control.test.ts

@@ -0,0 +1,28 @@
+import { describe, expect, it } from "vitest";
+import { sanitizeWorkspaceRuntimeControlTarget } from "./workspace-runtime-control";
+
+describe("sanitizeWorkspaceRuntimeControlTarget", () => {
+  it("drops unexpected keys while preserving the selected runtime target", () => {
+    const sanitized = sanitizeWorkspaceRuntimeControlTarget({
+      workspaceCommandId: "web",
+      runtimeServiceId: "service-1",
+      serviceIndex: 2,
+      ...( { action: "start" } as Record<string, unknown> ),
+    });
+
+    expect(sanitized).toEqual({
+      workspaceCommandId: "web",
+      runtimeServiceId: "service-1",
+      serviceIndex: 2,
+    });
+    expect("action" in sanitized).toBe(false);
+  });
+
+  it("normalizes an omitted target to nullable fields", () => {
+    expect(sanitizeWorkspaceRuntimeControlTarget()).toEqual({
+      workspaceCommandId: null,
+      runtimeServiceId: null,
+      serviceIndex: null,
+    });
+  });
+});

ui/src/api/workspace-runtime-control.ts

@@ -0,0 +1,11 @@
+import type { WorkspaceRuntimeControlTarget } from "@paperclipai/shared";
+
+export function sanitizeWorkspaceRuntimeControlTarget(
+  target: WorkspaceRuntimeControlTarget = {},
+): WorkspaceRuntimeControlTarget {
+  return {
+    workspaceCommandId: target.workspaceCommandId ?? null,
+    runtimeServiceId: target.runtimeServiceId ?? null,
+    serviceIndex: target.serviceIndex ?? null,
+  };
+}