Figured it out. In the working copy, I selected the root directory of the branch and clicked "Merge" from the top toolbar of Cornerstone. The option "Synchronize branch" is selected in the merge interface, and Cornerstone performs a dry start of the merge and displays a preview of all the files that it will merge with the trunk (there is a "Merge from" field, the default root directory of the trunk is used, ^ / trunk). From here, just “Merge Changes” was clicked, and the branch was updated with all changed files.