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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?
I loved the behavior of the checkboxes... you check a file in Unstaged, it moves to Staged. Then vice-versa. That made perfect sense. That's how I selected certain files to be staged or unstaged. The relationships were completely obvious because Unstaged was always on top of Staged, and I could see them move back and forth. Even if there's more files than would fit in each section, I could tell that the list changed. The number of files you've changed isn't SourceTree's issue, that's yours.
Now, I have to click to select each file, then hit the spacebar or click a button to move them... which is more steps and still removes them from one list and puts them on the other. For some reason this is only required on Windows; the Mac version has the checkboxes, which I used often.
I'm not understanding the complaint here or the change... the exact same thing happens when you stage/unstage, it's just more steps now. The checkboxes made things obvious and easier.
This isn't stack exchange, you probably won't have your post locked if it isn't a question.
On the other hand, most members of this site are Atlassian users - the devs are far too busy to read all of the questions. If you have a specific request for a change, you can post it at jira.atlassian.com, or vote up an existing bug report/feature request if there is one already making the same point.