A recent update to SourceTree gave us a checkbox next to not just files to commit, but also next to globel effect entries like Staged files and Unstaged files. When you uncheck them entries appear to disappear. If you had the preference "confirm before adding/removing files" checked, SourceTree would pop a foreground alert asking if you meant what you just did, for each and every individual file. Normal OS X style Multiple select doesn't appear to work, so you can't select a bunch of files and then check one, you have to use the "Staged files" and "Unstaged Files" entries for that. And sometimes the app gets confused and loses some of the changes if you have the confirm option turned on; they come back when I disable the confirm option.
What does this change improve? I see how clicking on the Unstaged files checkbox affects many files, but the relationships aren't immediately obvious and it took a bit of experimentation to figure out what you folks are doing. There's no horizontal differentiation between the Staged/Unstaged entries and the affected files; shouldn't the file entries, including checkboxes, at least be indented?