diff --git a/packages/core/src/config/config.ts b/packages/core/src/config/config.ts
index c6b01eec34..e52a286e7a 100644
--- a/packages/core/src/config/config.ts
+++ b/packages/core/src/config/config.ts
@@ -1288,15 +1288,18 @@ export class Config implements McpContext, AgentLoopContext {
     // Initialize centralized FileDiscoveryService
     const discoverToolsHandle = startupProfiler.start('discover_tools');
     this.getFileService();
+    if (this.getCheckpointingEnabled()) {
+      await this.getGitService();
+    }
     this._promptRegistry = new PromptRegistry();
     this._resourceRegistry = new ResourceRegistry();
 
     this.agentRegistry = new AgentRegistry(this);
-    const agentInitPromise = this.agentRegistry.initialize();
+    await this.agentRegistry.initialize();
 
     coreEvents.on(CoreEvent.AgentsRefreshed, this.onAgentsRefreshed);
 
-    this._toolRegistry = await this.createToolRegistry(agentInitPromise);
+    this._toolRegistry = await this.createToolRegistry();
     discoverToolsHandle?.end();
     this.mcpClientManager = new McpClientManager(
       this.clientVersion,
@@ -3154,33 +3157,13 @@ export class Config implements McpContext, AgentLoopContext {
     );
   }
 
-  async createToolRegistry(
-    agentInitPromise: Promise<void> = Promise.resolve(),
-  ): Promise<ToolRegistry> {
+  async createToolRegistry(): Promise<ToolRegistry> {
     const registry = new ToolRegistry(
       this,
       this.messageBus,
       /* isMainRegistry= */ true,
     );
 
-    // 1. Kick off concurrent background checks and external processes
-    const discoverAllToolsPromise = registry.discoverAllTools();
-    const useRipgrepPromise = this.getUseRipgrep()
-      ? canUseRipgrep()
-          .then((res) => ({ useRipgrep: res, errorString: undefined }))
-          .catch((error: unknown) => ({
-            useRipgrep: false,
-            errorString: String(error),
-          }))
-      : Promise.resolve({ useRipgrep: false, errorString: undefined });
-
-    // 2. Synchronize all heavy operations before registering dependent tools
-    const [_, rgResult] = await Promise.all([
-      agentInitPromise,
-      useRipgrepPromise,
-      discoverAllToolsPromise,
-    ]);
-
     // helper to create & register core tools that are enabled
     const maybeRegister = (
       toolClass: { name: string; Name?: string },
@@ -3216,17 +3199,19 @@ export class Config implements McpContext, AgentLoopContext {
     );
 
     if (this.getUseRipgrep()) {
-      if (rgResult.useRipgrep) {
+      let useRipgrep = false;
+      let errorString: undefined | string = undefined;
+      try {
+        useRipgrep = await canUseRipgrep();
+      } catch (error: unknown) {
+        errorString = String(error);
+      }
+      if (useRipgrep) {
         maybeRegister(RipGrepTool, () =>
           registry.registerTool(new RipGrepTool(this, this.messageBus)),
         );
       } else {
-        if (rgResult.errorString !== undefined) {
-          logRipgrepFallback(
-            this,
-            new RipgrepFallbackEvent(rgResult.errorString),
-          );
-        }
+        logRipgrepFallback(this, new RipgrepFallbackEvent(errorString));
         maybeRegister(GrepTool, () =>
           registry.registerTool(new GrepTool(this, this.messageBus)),
         );
@@ -3306,6 +3291,7 @@ export class Config implements McpContext, AgentLoopContext {
     // Register Subagents as Tools
     this.registerSubAgentTools(registry);
 
+    await registry.discoverAllTools();
     registry.sortTools();
     return registry;
   }