fix: improve MCP tool probing reliability

- Increase default probe timeout from 10s to 30s to handle slow
  package managers (uvx, npx) that install on first run
- Add console logging for probe success/failure to aid debugging
- Probe manually configured MCP servers (not just discovered ones)
  so all servers with wildcard tools get their tools discovered

Co-authored-by: Copilot <223556219+Copilot@users.noreply.github.com>

src/main/AryxAppService.ts

@@ -2130,10 +2130,14 @@ export class AryxAppService extends EventEmitter<AppServiceEvents> {
   }
 
   private async probeAllAcceptedMcpServers(workspace: WorkspaceState): Promise<void> {
+    // Probe discovered MCP servers (from config files)
     await this.probeDiscoveredMcpServersFromState(workspace.settings.discoveredUserTooling);
     for (const project of workspace.projects) {
       await this.probeDiscoveredMcpServersFromState(project.discoveredTooling);
     }
+
+    // Probe manually configured MCP servers that have empty tools arrays
+    await this.probeManualMcpServers(workspace);
   }
 
   private async probeDiscoveredMcpServersFromState(
@@ -2185,6 +2189,30 @@ export class AryxAppService extends EventEmitter<AppServiceEvents> {
     }
   }
 
+  private async probeManualMcpServers(workspace: WorkspaceState): Promise<void> {
+    const manualServers = workspace.settings.tooling.mcpServers.filter(
+      (server) => server.tools.length === 0 && (!server.probedTools || server.probedTools.length === 0),
+    );
+    if (manualServers.length === 0) return;
+
+    const tokenLookup = (url: string) => getStoredToken(url)?.accessToken;
+    const results = await probeServers(manualServers, tokenLookup);
+
+    let changed = false;
+    for (const result of results) {
+      if (result.status !== 'success' || result.tools.length === 0) continue;
+      const server = workspace.settings.tooling.mcpServers.find((s) => s.id === result.serverId);
+      if (server) {
+        server.probedTools = result.tools;
+        changed = true;
+      }
+    }
+
+    if (changed) {
+      await this.persistAndBroadcast(workspace);
+    }
+  }
+
   private discoveredServerToDefinition(server: DiscoveredMcpServer): McpServerDefinition {
     if (server.transport === 'local') {
       return {

src/main/services/mcpToolProber.ts

@@ -19,7 +19,7 @@ export interface McpProbeResult {
 }
 
 const CLIENT_INFO = { name: 'aryx', version: '1.0.0' };
-const DEFAULT_TIMEOUT_MS = 10_000;
+const DEFAULT_TIMEOUT_MS = 30_000;
 const MAX_CONCURRENCY = 5;
 
 export async function probeServers(
@@ -65,6 +65,7 @@ export async function probeServer(
       `Probe timed out after ${timeoutMs}ms`,
     );
 
+    console.log(`[aryx mcp-probe] ${server.name}: discovered ${tools.length} tool(s)`);
     return {
       serverId: server.id,
       serverName: server.name,
@@ -72,12 +73,14 @@ export async function probeServer(
       status: 'success',
     };
   } catch (error) {
+    const message = error instanceof Error ? error.message : String(error);
+    console.warn(`[aryx mcp-probe] ${server.name}: failed — ${message}`);
     return {
       serverId: server.id,
       serverName: server.name,
       tools: [],
       status: 'failed',
-      error: error instanceof Error ? error.message : String(error),
+      error: message,
     };
   }
 }