[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>

server/src/services/execution-workspaces.ts

@@ -192,6 +192,11 @@ export function readExecutionWorkspaceConfig(metadata: Record<string, unknown> |
     cleanupCommand: readNullableString(raw.cleanupCommand),
     workspaceRuntime: cloneRecord(raw.workspaceRuntime),
     desiredState: raw.desiredState === "running" || raw.desiredState === "stopped" ? raw.desiredState : null,
+    serviceStates: isRecord(raw.serviceStates)
+      ? Object.fromEntries(
+          Object.entries(raw.serviceStates).filter(([, state]) => state === "running" || state === "stopped"),
+        ) as ExecutionWorkspaceConfig["serviceStates"]
+      : null,
   };
 
   const hasConfig = Object.values(config).some((value) => {
@@ -214,6 +219,7 @@ export function mergeExecutionWorkspaceConfig(
     cleanupCommand: null,
     workspaceRuntime: null,
     desiredState: null,
+    serviceStates: null,
   };
 
   if (patch === null) {
@@ -232,6 +238,14 @@ export function mergeExecutionWorkspaceConfig(
           ? patch.desiredState
           : null
         : current.desiredState,
+    serviceStates:
+      patch.serviceStates !== undefined && isRecord(patch.serviceStates)
+        ? Object.fromEntries(
+            Object.entries(patch.serviceStates).filter(([, state]) => state === "running" || state === "stopped"),
+          ) as ExecutionWorkspaceConfig["serviceStates"]
+        : patch.serviceStates !== undefined
+          ? null
+          : current.serviceStates,
   };
 
   const hasConfig = Object.values(nextConfig).some((value) => {
@@ -247,6 +261,7 @@ export function mergeExecutionWorkspaceConfig(
       cleanupCommand: nextConfig.cleanupCommand,
       workspaceRuntime: nextConfig.workspaceRuntime,
       desiredState: nextConfig.desiredState,
+      serviceStates: nextConfig.serviceStates ?? null,
     };
   } else {
     delete nextMetadata.config;