[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>

scripts/provision-worktree.sh

@@ -53,6 +53,24 @@ run_paperclipai_command() {
   return 1
 }
 
+paperclipai_command_available() {
+  if command -v pnpm >/dev/null 2>&1 && pnpm paperclipai --help >/dev/null 2>&1; then
+    return 0
+  fi
+
+  local base_cli_tsx_path="$base_cwd/cli/node_modules/tsx/dist/cli.mjs"
+  local base_cli_entry_path="$base_cwd/cli/src/index.ts"
+  if command -v node >/dev/null 2>&1 && [[ -f "$base_cli_tsx_path" ]] && [[ -f "$base_cli_entry_path" ]]; then
+    return 0
+  fi
+
+  if command -v paperclipai >/dev/null 2>&1; then
+    return 0
+  fi
+
+  return 1
+}
+
 run_isolated_worktree_init() {
   run_paperclipai_command \
     worktree \
@@ -318,7 +336,9 @@ main().catch((error) => {
 EOF
 }
 
-if ! run_isolated_worktree_init; then
+if paperclipai_command_available; then
+  run_isolated_worktree_init
+else
   echo "paperclipai CLI not available in this workspace; writing isolated fallback config without DB seeding." >&2
   write_fallback_worktree_config
 fi
@@ -384,14 +404,49 @@ if [[ -f "$worktree_cwd/package.json" && -f "$worktree_cwd/pnpm-lock.yaml" ]]; t
       done
     }
 
-    (
-      cd "$worktree_cwd"
-      pnpm install --frozen-lockfile
-    ) || {
-      restore_moved_symlinks
-      exit 1
+    run_pnpm_install() {
+      local stdout_path stderr_path
+      stdout_path="$(mktemp)"
+      stderr_path="$(mktemp)"
+
+      if (
+        cd "$worktree_cwd"
+        pnpm install "$@"
+      ) >"$stdout_path" 2>"$stderr_path"; then
+        cat "$stdout_path"
+        cat "$stderr_path" >&2
+        rm -f "$stdout_path" "$stderr_path"
+        return 0
+      fi
+
+      local exit_code=$?
+      cat "$stdout_path"
+      cat "$stderr_path" >&2
+      if grep -q "ERR_PNPM_OUTDATED_LOCKFILE" "$stdout_path" "$stderr_path"; then
+        rm -f "$stdout_path" "$stderr_path"
+        return 90
+      fi
+
+      rm -f "$stdout_path" "$stderr_path"
+      return "$exit_code"
     }
 
+    if run_pnpm_install --frozen-lockfile; then
+      :
+    else
+      install_exit_code=$?
+      if [[ "$install_exit_code" -eq 90 ]]; then
+        echo "pnpm-lock.yaml is out of date in this execution workspace; retrying install without --frozen-lockfile." >&2
+        run_pnpm_install --no-frozen-lockfile || {
+          restore_moved_symlinks
+          exit 1
+        }
+      else
+        restore_moved_symlinks
+        exit "$install_exit_code"
+      fi
+    fi
+
     cleanup_moved_symlinks
   fi