I have had this happen to me often. I am working on a master branch and I need to test a plugin, so I create a new branch and check it out. I download the plugin into the pr
git will not remove untracked files from your working copy, so unless you added the files of the plugin and created a commit on the new branch git will not do anything to your plugin files.
if you want to remove untracked file from your working tree, use git clean – be careful, it will remove any untracked file from disk and there's no way to recover from that (without using undelete software)