[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>

packages/shared/src/workspace-commands.test.ts

@@ -0,0 +1,56 @@
+import { describe, expect, it } from "vitest";
+import {
+  findWorkspaceCommandDefinition,
+  listWorkspaceCommandDefinitions,
+  matchWorkspaceRuntimeServiceToCommand,
+} from "./workspace-commands.js";
+
+describe("workspace command helpers", () => {
+  it("derives service and job commands from command-first runtime config", () => {
+    const commands = listWorkspaceCommandDefinitions({
+      commands: [
+        { id: "web", name: "web", kind: "service", command: "pnpm dev" },
+        { id: "db-migrate", name: "db:migrate", kind: "job", command: "pnpm db:migrate" },
+      ],
+    });
+
+    expect(commands).toEqual([
+      expect.objectContaining({ id: "web", kind: "service", serviceIndex: 0 }),
+      expect.objectContaining({ id: "db-migrate", kind: "job", serviceIndex: null }),
+    ]);
+  });
+
+  it("falls back to legacy services and jobs arrays", () => {
+    const commands = listWorkspaceCommandDefinitions({
+      services: [{ name: "web", command: "pnpm dev" }],
+      jobs: [{ name: "lint", command: "pnpm lint" }],
+    });
+
+    expect(commands).toEqual([
+      expect.objectContaining({ id: "service:web", kind: "service", serviceIndex: 0 }),
+      expect.objectContaining({ id: "job:lint", kind: "job", serviceIndex: null }),
+    ]);
+  });
+
+  it("matches a configured service command to the current runtime service", () => {
+    const workspaceRuntime = {
+      commands: [
+        { id: "web", name: "web", kind: "service", command: "pnpm dev", cwd: "." },
+      ],
+    };
+    const command = findWorkspaceCommandDefinition(workspaceRuntime, "web");
+    expect(command).not.toBeNull();
+
+    const match = matchWorkspaceRuntimeServiceToCommand(command!, [
+      {
+        id: "runtime-web",
+        serviceName: "web",
+        command: "pnpm dev",
+        cwd: "/repo",
+        configIndex: null,
+      },
+    ]);
+
+    expect(match).toEqual(expect.objectContaining({ id: "runtime-web" }));
+  });
+});