Encrypting filenames is an interesting idea, but also doesn't really seem that useful in practice to me.

Most projects or directories probably don't contain filenames that are sensitive. If you do have sensitive filenames, storing the true filenames in an encrypted manifest will work fine if you don't have a huge number of files.

For the use case where you have a lot of data, the data needs to be encrypted, and the filenames are sensitive you'd surely be better off using something like dm-crypt (if you can use a block device) or a FUSE solution like gocryptfs.