merge: resolve conflicts with main (PR #293)

Keep our fixes over the merged auto-repair PR:
- plugin_manager: backup dir skip + clear-before-update
- state_reconciliation: no skip on missing 'enabled', default True
- store_manager: resolved_id for monorepo migration
- app.py: reconciliation threading lock + return type

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

src/plugin_system/plugin_manager.py

@@ -119,6 +119,9 @@ class PluginManager:
             for item in directory.iterdir():
                 if not item.is_dir():
                     continue
+                # Skip backup directories so they don't overwrite live entries
+                if '.standalone-backup-' in item.name:
+                    continue
 
                 manifest_path = item / "manifest.json"
                 if manifest_path.exists():
@@ -136,11 +139,14 @@ class PluginManager:
         except (OSError, PermissionError) as e:
             self.logger.error("Error scanning directory %s: %s", directory, e, exc_info=True)
 
-        # Update shared state under lock
+        # Replace shared state under lock so uninstalled plugins don't linger
         with self._discovery_lock:
+            self.plugin_manifests.clear()
             self.plugin_manifests.update(new_manifests)
             if not hasattr(self, 'plugin_directories'):
                 self.plugin_directories = {}
+            else:
+                self.plugin_directories.clear()
             self.plugin_directories.update(new_directories)
 
         return plugin_ids

src/plugin_system/state_reconciliation.py

@@ -182,10 +182,8 @@ class StateReconciliation:
                     continue
                 if plugin_id in self._SYSTEM_CONFIG_KEYS:
                     continue
-                if 'enabled' not in plugin_config:
-                    continue
                 state[plugin_id] = {
-                    'enabled': plugin_config.get('enabled', False),
+                    'enabled': plugin_config.get('enabled', True),
                     'version': plugin_config.get('version'),
                     'exists_in_config': True
                 }

src/plugin_system/store_manager.py

@@ -1785,11 +1785,13 @@ class PluginStoreManager:
                 self.fetch_registry(force_refresh=True)
                 plugin_info_remote = self.get_plugin_info(plugin_id, fetch_latest_from_github=True, force_refresh=True)
                 # Try without 'ledmatrix-' prefix (monorepo migration)
+                resolved_id = plugin_id
                 if not plugin_info_remote and plugin_id.startswith('ledmatrix-'):
                     alt_id = plugin_id[len('ledmatrix-'):]
                     plugin_info_remote = self.get_plugin_info(alt_id, fetch_latest_from_github=True, force_refresh=True)
                     if plugin_info_remote:
-                        self.logger.info(f"Plugin {plugin_id} found in registry as {alt_id}")
+                        resolved_id = alt_id
+                        self.logger.info(f"Plugin {plugin_id} found in registry as {resolved_id}")
                 remote_branch = None
                 remote_sha = None
 
@@ -1804,13 +1806,13 @@ class PluginStoreManager:
                     local_remote = git_info.get('remote_url', '')
                     if local_remote and registry_repo and self._normalize_repo_url(local_remote) != self._normalize_repo_url(registry_repo):
                         self.logger.info(
-                            f"Plugin {plugin_id} git remote ({local_remote}) differs from registry ({registry_repo}). "
+                            f"Plugin {resolved_id} git remote ({local_remote}) differs from registry ({registry_repo}). "
                             f"Reinstalling from registry to migrate to new source."
                         )
                         if not self._safe_remove_directory(plugin_path):
-                            self.logger.error(f"Failed to remove old plugin directory for {plugin_id}")
+                            self.logger.error(f"Failed to remove old plugin directory for {resolved_id}")
                             return False
-                        return self.install_plugin(plugin_id)
+                        return self.install_plugin(resolved_id)
 
                     # Check if already up to date
                     if remote_sha and local_sha and remote_sha.startswith(local_sha):

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:
+    with _reconciliation_lock:
-        _reconciliation_started = True
+        if not _reconciliation_started:
-        import threading
+            _reconciliation_started = True
-        threading.Thread(target=_run_startup_reconciliation, daemon=True).start()
+            _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

@@ -401,9 +401,15 @@
             if (content && !content.hasAttribute('data-loaded')) {
                 content.setAttribute('data-loaded', 'true');
                 console.log('Loading plugins directly via fetch (HTMX fallback)...');
-                fetch('/v3/partials/plugins')
+                const controller = new AbortController();
-                    .then(r => r.text())
+                const timeout = setTimeout(() => controller.abort(), 10000);
+                fetch('/v3/partials/plugins', { signal: controller.signal })
+                    .then(r => {
+                        if (!r.ok) throw new Error(r.status + ' ' + r.statusText);
+                        return r.text();
+                    })
                     .then(html => {
+                        clearTimeout(timeout);
                         content.innerHTML = html;
                         // Trigger full initialization chain
                         if (window.pluginManager) {
@@ -415,6 +421,7 @@
                         }
                     })
                     .catch(err => {
+                        clearTimeout(timeout);
                         console.error('Failed to load plugins:', err);
                         content.removeAttribute('data-loaded');
                         content.innerHTML = '<div class="bg-red-50 border border-red-200 rounded-lg p-4"><p class="text-red-800">Failed to load Plugin Manager. Please refresh the page.</p></div>';
@@ -426,13 +433,9 @@
         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()"]');
+                // Load plugins tab content directly regardless of active tab,
-                if (appElement && appElement._x_dataStack && appElement._x_dataStack[0]) {
+                // so it's ready when the user navigates to it
-                    const activeTab = appElement._x_dataStack[0].activeTab;
+                loadPluginsDirect();
-                    if (activeTab === 'plugins') {
-                        loadPluginsDirect();
-                    }
-                }
             }
         }, 5000);
     </script>
@@ -976,7 +979,7 @@
             <!-- 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
@@ -1170,7 +1173,7 @@
             <!-- Plugins tab -->
             <div x-show="activeTab === 'plugins'" x-transition>
                 <div id="plugins-content" hx-get="/v3/partials/plugins" hx-trigger="revealed" hx-swap="innerHTML"
-                     hx-on::htmx:response-error="loadPluginsDirect()">
+                     hx-on::response-error="loadPluginsDirect()">
                     <div class="animate-pulse">
                         <div class="bg-white rounded-lg shadow p-6">
                             <div class="h-4 bg-gray-200 rounded w-1/4 mb-4"></div>