fix(ui): improve React Query hooks and fix edge cases

- Update query keys to include all relevant parameters (branches, agents)
- Fix use-branches to pass includeRemote parameter to query key
- Fix use-settings to include sources in agents query key
- Update running-agents-view to use correct query key structure
- Update use-spec-loading to properly use spec query hooks
- Add missing queryClient invalidation in auto-mode mutations
- Add missing cache invalidation in spec mutations after creation

Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>

apps/ui/src/components/usage-popover.tsx

@@ -304,7 +304,7 @@ export function UsagePopover() {
                   variant="ghost"
                   size="icon"
                   className={cn('h-6 w-6', claudeLoading && 'opacity-80')}
-                  onClick={() => !claudeLoading && fetchClaudeUsage(false)}
+                  onClick={() => !claudeLoading && fetchClaudeUsage()}
                 >
                   <RefreshCw className="w-3.5 h-3.5" />
                 </Button>
@@ -411,7 +411,7 @@ export function UsagePopover() {
                   variant="ghost"
                   size="icon"
                   className={cn('h-6 w-6', codexLoading && 'opacity-80')}
-                  onClick={() => !codexLoading && fetchCodexUsage(false)}
+                  onClick={() => !codexLoading && fetchCodexUsage()}
                 >
                   <RefreshCw className="w-3.5 h-3.5" />
                 </Button>