fix: address CodeRabbit review findings across plugin system

- plugin_manager.py: clear plugin_manifests/plugin_directories before update
  to prevent ghost entries for uninstalled plugins persisting across scans
- state_reconciliation.py: remove 'enabled' key check that skipped legacy
  plugin configs, default to enabled=True matching PluginManager.load_plugin
- app.py: add threading.Lock around reconciliation start guard to prevent
  race condition spawning duplicate threads; add -> None return annotation
- store_manager.py: use resolved registry ID (alt_id) instead of original
  plugin_id when reinstalling during monorepo migration
- base.html: check Response.ok in loadPluginsDirect fallback; trigger
  fallback on tab click when HTMX unavailable; remove active-tab check
  from 5-second timeout so content preloads regardless

Skipped: api_v3.py secret redaction suggestion — the caller at line 2539
already tries schema-based mask_secret_fields() before falling back to
_conservative_mask_config, making the suggested change redundant.

Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>

web_interface/app.py

@@ -653,8 +653,10 @@ def _initialize_health_monitor():
 
 _reconciliation_done = False
 _reconciliation_started = False
+import threading as _threading
+_reconciliation_lock = _threading.Lock()
 
-def _run_startup_reconciliation():
+def _run_startup_reconciliation() -> None:
     """Run state reconciliation in background to auto-repair missing plugins."""
     global _reconciliation_done, _reconciliation_started
     from src.logging_config import get_logger
@@ -678,10 +680,12 @@ def _run_startup_reconciliation():
             _reconciliation_done = True
         else:
             _logger.warning("[Reconciliation] Finished with unresolved issues, will retry")
-            _reconciliation_started = False
+            with _reconciliation_lock:
+                _reconciliation_started = False
     except Exception as e:
         _logger.error("[Reconciliation] Error: %s", e, exc_info=True)
-        _reconciliation_started = False
+        with _reconciliation_lock:
+            _reconciliation_started = False
 
 # Initialize health monitor and run reconciliation on first request
 @app.before_request
@@ -690,10 +694,10 @@ def check_health_monitor():
     global _reconciliation_started
     if not _health_monitor_initialized:
         _initialize_health_monitor()
-    if not _reconciliation_started:
-        _reconciliation_started = True
-        import threading
-        threading.Thread(target=_run_startup_reconciliation, daemon=True).start()
+    with _reconciliation_lock:
+        if not _reconciliation_started:
+            _reconciliation_started = True
+            _threading.Thread(target=_run_startup_reconciliation, daemon=True).start()
 
 if __name__ == '__main__':
     app.run(host='0.0.0.0', port=5000, debug=True)

web_interface/templates/v3/base.html

@@ -402,7 +402,10 @@
                 content.setAttribute('data-loaded', 'true');
                 console.log('Loading plugins directly via fetch (HTMX fallback)...');
                 fetch('/v3/partials/plugins')
-                    .then(r => r.text())
+                    .then(r => {
+                        if (!r.ok) throw new Error(r.status + ' ' + r.statusText);
+                        return r.text();
+                    })
                     .then(html => {
                         content.innerHTML = html;
                         // Trigger full initialization chain
@@ -426,13 +429,9 @@
         setTimeout(() => {
             if (typeof htmx === 'undefined') {
                 console.warn('HTMX not loaded after 5 seconds, using direct fetch for plugins');
-                const appElement = document.querySelector('[x-data="app()"]');
-                if (appElement && appElement._x_dataStack && appElement._x_dataStack[0]) {
-                    const activeTab = appElement._x_dataStack[0].activeTab;
-                    if (activeTab === 'plugins') {
-                        loadPluginsDirect();
-                    }
-                }
+                // Load plugins tab content directly regardless of active tab,
+                // so it's ready when the user navigates to it
+                loadPluginsDirect();
             }
         }, 5000);
     </script>
@@ -976,7 +975,7 @@
             <!-- Second row - Plugin tabs (populated dynamically) -->
             <div id="plugin-tabs-row" class="border-b border-gray-200">
                 <nav class="-mb-px flex flex-wrap gap-y-2 gap-x-2 lg:gap-x-3 xl:gap-x-4">
-                    <button @click="activeTab = 'plugins'"
+                    <button @click="activeTab = 'plugins'; if (typeof htmx === 'undefined') { $nextTick(() => loadPluginsDirect()); }"
                             :class="activeTab === 'plugins' ? 'nav-tab-active' : ''"
                             class="nav-tab">
                         <i class="fas fa-plug"></i>Plugin Manager