Fix SSHRuntime trunk branch handling

- Create local tracking branches for all remote refs after clone
- This ensures branch names work directly without needing 'origin/' prefix
- Simplify checkout command to use branch names directly
- Add debug logging to help diagnose issues

The issue was that after git clone from bundle, all branches exist as
origin/* remote refs. When we later remove the origin remote, these refs
disappear. By creating local tracking branches first, we ensure the branch
names are available for checkout operations, fixing the trunk branch
parameter handling.

Author: ammar-agent

src/runtime/SSHRuntime.ts

@@ -480,7 +480,21 @@ export class SSHRuntime implements Runtime {
         throw new Error(`Failed to clone repository: ${cloneStderr || cloneStdout}`);
       }
 
-      // Step 4: Update origin remote if we have an origin URL
+      // Step 4: Create local tracking branches for all remote branches
+      // This ensures that branch names like "custom-trunk" can be used directly
+      // in git checkout commands, rather than needing "origin/custom-trunk"
+      initLogger.logStep(`Creating local tracking branches...`);
+      const createTrackingBranchesStream = await this.exec(
+        `cd ${cloneDestPath} && for branch in $(git for-each-ref --format='%(refname:short)' refs/remotes/origin/ | grep -v 'origin/HEAD'); do localname=\${branch#origin/}; git show-ref --verify --quiet refs/heads/$localname || git branch $localname $branch; done`,
+        {
+          cwd: "~",
+          timeout: 30,
+        }
+      );
+      await createTrackingBranchesStream.exitCode;
+      // Don't fail if this fails - some branches may already exist
+
+      // Step 5: Update origin remote if we have an origin URL
       if (originUrl) {
         initLogger.logStep(`Setting origin remote to ${originUrl}...`);
         const setOriginStream = await this.exec(
@@ -689,10 +703,24 @@ export class SSHRuntime implements Runtime {
 
       // 2. Checkout branch remotely
       // If branch exists locally, check it out; otherwise create it from the specified trunk branch
-      // Note: After git clone from bundle, branches exist as origin/* refs, so we need to check both
-      // local branch and origin/branch when creating the new branch
+      // Note: We've already created local branches for all remote refs in syncProjectToRemote
       initLogger.logStep(`Checking out branch: ${branchName}`);
-      const checkoutCmd = `(git checkout ${shescape.quote(branchName)} 2>/dev/null || git checkout -b ${shescape.quote(branchName)} origin/${shescape.quote(trunkBranch)} 2>/dev/null || git checkout -b ${shescape.quote(branchName)} ${shescape.quote(trunkBranch)})`;
+
+      // DEBUG: Log git state after clone
+      initLogger.logStep(`[DEBUG] Inspecting git state after clone...`);
+      const debugStream = await this.exec(
+        `echo "=== Current branch ===" && git branch && echo "=== All branches ===" && git branch -a && echo "=== HEAD ===" && git rev-parse HEAD && echo "=== Files ===" && ls -la`,
+        { cwd: workspacePath, timeout: 30 }
+      );
+      const [debugOut] = await Promise.all([
+        streamToString(debugStream.stdout),
+        debugStream.exitCode,
+      ]);
+      initLogger.logStdout(debugOut);
+
+      // Try to checkout existing branch, or create new branch from trunk
+      // Since we've created local branches for all remote refs, we can use branch names directly
+      const checkoutCmd = `git checkout ${shescape.quote(branchName)} 2>/dev/null || git checkout -b ${shescape.quote(branchName)} ${shescape.quote(trunkBranch)}`;
 
       const checkoutStream = await this.exec(checkoutCmd, {
         cwd: workspacePath, // Use the full workspace path for git operations
@@ -716,6 +744,18 @@ export class SSHRuntime implements Runtime {
       }
       initLogger.logStep("Branch checked out successfully");
 
+      // DEBUG: Log git state after checkout
+      initLogger.logStep(`[DEBUG] Inspecting git state after checkout...`);
+      const debugStream2 = await this.exec(
+        `echo "=== Current branch ===" && git branch && echo "=== HEAD ===" && git rev-parse HEAD && echo "=== Files ===" && ls -la && echo "=== Last commits ===" && git log --oneline -5`,
+        { cwd: workspacePath, timeout: 30 }
+      );
+      const [debugOut2] = await Promise.all([
+        streamToString(debugStream2.stdout),
+        debugStream2.exitCode,
+      ]);
+      initLogger.logStdout(debugOut2);
+
       // 3. Run .cmux/init hook if it exists
       // Note: runInitHook calls logComplete() internally if hook exists
       const hookExists = await checkInitHookExists(projectPath);