Fix SSH trunk branch: ensure trunk is checked out before creating branch

The previous fix used 'git checkout -b branch trunk' which failed because
after git clone from bundle, the trunk branch exists as a ref but may not
be properly resolved. This caused new branches to be created from the wrong
base.

New approach:
1. Try to checkout the branch if it already exists
2. If not found, first checkout the trunk branch explicitly
3. Then create the new branch from HEAD (which is now at trunk)

This ensures the trunk branch is properly resolved and checked out before
creating the new branch from it.

Author: ammar-agent

src/runtime/SSHRuntime.ts

@@ -688,13 +688,50 @@ export class SSHRuntime implements Runtime {
       initLogger.logStep("Files synced successfully");
 
       // 2. Checkout branch remotely
-      // If branch exists, check it out; otherwise create it from the specified trunk branch
+      // If branch doesn't exist, we need to ensure the trunk branch is checked out locally first
+      // to properly resolve it when creating the new branch
       initLogger.logStep(`Checking out branch: ${branchName}`);
-      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
-        timeout: 300, // 5 minutes for git checkout (can be slow on large repos)
+      // First, try to checkout the branch if it already exists
+      const tryCheckout = await this.exec(
+        `git checkout ${shescape.quote(branchName)} 2>/dev/null || echo "branch_not_found"`,
+        {
+          cwd: workspacePath,
+          timeout: 60,
+        }
+      );
+      const checkoutResult = await streamToString(tryCheckout.stdout);
+
+      // If branch doesn't exist, ensure trunk is available then create from it
+      if (checkoutResult.includes("branch_not_found")) {
+        // Ensure the trunk branch ref is available (checkout to resolve it)
+        await this.exec(`git checkout ${shescape.quote(trunkBranch)}`, {
+          cwd: workspacePath,
+          timeout: 60,
+        });
+
+        // Now create the new branch from the checked-out trunk
+        const createStream = await this.exec(`git checkout -b ${shescape.quote(branchName)}`, {
+          cwd: workspacePath,
+          timeout: 60,
+        });
+
+        const exitCode = await createStream.exitCode;
+        if (exitCode !== 0) {
+          const stderr = await streamToString(createStream.stderr);
+          initLogger.logStderr(`Failed to create branch from trunk: ${stderr}`);
+          initLogger.logComplete(-1);
+          return {
+            success: false,
+            error: `Failed to create branch from trunk: ${stderr}`,
+          };
+        }
+      }
+
+      // At this point, we should be on the correct branch
+      const checkoutStream = await this.exec(`git branch --show-current`, {
+        cwd: workspacePath,
+        timeout: 10,
       });
 
       const [stdout, stderr, exitCode] = await Promise.all([