Thanks for your feedback. It's true that there are still edge cases where the repo can get in an inconsistent state. This is the biggest issue I need to address before the 1.0 release. I should be able to provide commands that will fix up the repo if this happens. And thanks for pointing me in the direction of rebases - I clearly haven't done enough testing with them.

As for security, .gitattributes actually does have negation capability (see the article for an example) so you can encrypt the whole repo by default and explicitly whitelist files to not be encrypted. But I must emphasize that if you are encrypting most or all of the files in your repo, git-crypt is not the best tool because as you point out, git filters haven't really been designed for this. Where git-crypt really shines is where most of your repo is public, but you have a few files (perhaps private keys named *.key, or a file with API credentials) which you need to encrypt. I do like your suggestion of a command to check if a file is being encrypted, and plan to implement that.