[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/lib/keyboardShortcuts.ts

@@ -12,6 +12,7 @@ const PAGE_SEARCH_SHORTCUT_SELECTOR = "[data-page-search-target='true']";
 const MODIFIER_ONLY_KEYS = new Set(["Shift", "Meta", "Control", "Alt"]);
 
 export type InboxQuickArchiveKeyAction = "ignore" | "archive" | "disarm";
+export type InboxUndoArchiveKeyAction = "ignore" | "undo_archive";
 export type IssueDetailGoKeyAction = "ignore" | "arm" | "navigate_inbox" | "focus_comment" | "disarm";
 
 export function isKeyboardShortcutTextInputTarget(target: EventTarget | null): boolean {
@@ -105,6 +106,33 @@ export function resolveInboxQuickArchiveKeyAction({
   return "ignore";
 }
 
+export function resolveInboxUndoArchiveKeyAction({
+  hasUndoableArchive,
+  defaultPrevented,
+  key,
+  metaKey,
+  ctrlKey,
+  altKey,
+  target,
+  hasOpenDialog,
+}: {
+  hasUndoableArchive: boolean;
+  defaultPrevented: boolean;
+  key: string;
+  metaKey: boolean;
+  ctrlKey: boolean;
+  altKey: boolean;
+  target: EventTarget | null;
+  hasOpenDialog: boolean;
+}): InboxUndoArchiveKeyAction {
+  if (!hasUndoableArchive) return "ignore";
+  if (defaultPrevented) return "ignore";
+  if (metaKey || ctrlKey || altKey || isModifierOnlyKey(key)) return "ignore";
+  if (hasOpenDialog || isKeyboardShortcutTextInputTarget(target)) return "ignore";
+  if (key === "u") return "undo_archive";
+  return "ignore";
+}
+
 export function resolveIssueDetailGoKeyAction({
   armed,
   defaultPrevented,