git-annex has a powerful syntax for making it act on only certain files.

The simplest thing is to exclude some files, using wild cards:

git annex get --exclude '*.mp3' --exclude '*.ogg'

But you can also exclude files that git-annex's location tracking information indicates are present in a given repository. For example, if you want to populate newarchive with files, but not those already on oldarchive, you could do it like this:

git annex copy --not --in oldarchive --to newarchive

Without the --not, --in makes it act on files that are in the specified repository. So, to remove files that are on oldarchive:

git annex drop --in oldarchive

Or maybe you're curious which files have a lot of copies, and then also want to know which files have only one copy:

git annex find --copies 7
git annex find --not --copies 2

The above are the simple examples of specifying what files git-annex should act on. But you can specify anything you can dream up by combining the things above, with --and --or -( and -). Those last two strange-looking options are parentheses, for grouping other options. You will probably have to escape them from your shell.

Here are the mp3 files that are in either of two repositories, but have less than 3 copies:

git annex find --not --exclude '*.mp3' --and \
    -\( --in usbdrive --or --in archive -\) --and \
    --not --copies 3