In my analyses I often have multiple (>10k) generated small files in a single directory.

I would like to store this in git annex, in order to version them and probably even synchronize. The problem is that if a huge number of files is stored inside the repository, the repository itself becomes huge and slow. There are some ways to improve the performance (1, 2, 3), but it doesn't solve the issue completely.

I was wondering if it is possible to force git annex to treat a single directory with multiple files as a single item? Probably with abandoning the checksum verification.