[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/validators/execution-workspace.ts

@@ -14,6 +14,13 @@ export const executionWorkspaceConfigSchema = z.object({
   cleanupCommand: z.string().optional().nullable(),
   workspaceRuntime: z.record(z.unknown()).optional().nullable(),
   desiredState: z.enum(["running", "stopped"]).optional().nullable(),
+  serviceStates: z.record(z.enum(["running", "stopped"])).optional().nullable(),
+}).strict();
+
+export const workspaceRuntimeControlTargetSchema = z.object({
+  workspaceCommandId: z.string().min(1).optional().nullable(),
+  runtimeServiceId: z.string().uuid().optional().nullable(),
+  serviceIndex: z.number().int().nonnegative().optional().nullable(),
 }).strict();
 
 export const executionWorkspaceCloseReadinessStateSchema = z.enum([
@@ -88,6 +95,7 @@ export const workspaceRuntimeServiceSchema = z.object({
   stoppedAt: z.coerce.date().nullable(),
   stopPolicy: z.record(z.unknown()).nullable(),
   healthStatus: z.enum(["unknown", "healthy", "unhealthy"]),
+  configIndex: z.number().int().nonnegative().nullable().optional(),
   createdAt: z.coerce.date(),
   updatedAt: z.coerce.date(),
 }).strict();

packages/shared/src/validators/index.ts

@@ -32,6 +32,11 @@ export {
   upsertIssueFeedbackVoteSchema,
   type UpsertIssueFeedbackVote,
 } from "./feedback.js";
+export {
+  sidebarOrderPreferenceSchema,
+  upsertSidebarOrderPreferenceSchema,
+  type UpsertSidebarOrderPreference,
+} from "./sidebar-preferences.js";
 export {
   companySkillSourceTypeSchema,
   companySkillTrustLevelSchema,

packages/shared/src/validators/project.ts

@@ -31,6 +31,7 @@ export const projectExecutionWorkspacePolicySchema = z
 export const projectWorkspaceRuntimeConfigSchema = z.object({
   workspaceRuntime: z.record(z.unknown()).optional().nullable(),
   desiredState: z.enum(["running", "stopped"]).optional().nullable(),
+  serviceStates: z.record(z.enum(["running", "stopped"])).optional().nullable(),
 }).strict();
 
 const projectWorkspaceSourceTypeSchema = z.enum(["local_path", "git_repo", "remote_managed", "non_git_path"]);

packages/shared/src/validators/sidebar-preferences.ts

@@ -0,0 +1,14 @@
+import { z } from "zod";
+
+const sidebarOrderedIdSchema = z.string().uuid();
+
+export const sidebarOrderPreferenceSchema = z.object({
+  orderedIds: z.array(sidebarOrderedIdSchema),
+  updatedAt: z.coerce.date().nullable(),
+});
+
+export const upsertSidebarOrderPreferenceSchema = z.object({
+  orderedIds: z.array(sidebarOrderedIdSchema),
+});
+
+export type UpsertSidebarOrderPreference = z.infer<typeof upsertSidebarOrderPreferenceSchema>;