I was working on a side branch in the Beta IDE. Then I clicked the “merge changes into master” button. The code appears to have merged successfully and the new, merged code (the master branch) shows up in the IDE. However, when I went to run the Debug version of the code, it was still stuck in the side branch prior to merging into master (and one or two subsequent changes to master).
It was a simple fix: change the branch back to the side branch, and then manually re-set the branch to master. Then running the app in Debug mode worked as expected. The hitch just threw me for a few minutes.