I use the standard Ubuntu eCryptfs setup to encrypt my home folder. As far as I can tell it encrypts the files and their names, but the directory hierarchy is essentially the same.
Every git repository contains the same
hooks folder with the exact same number of files. The
.git usually has the same number of files and folders in it. It should be possible to write a small script that searches for git repositories and tells you which the
hooks folder is and so on. Then you have only limited possibilities which hook is which, which might be even so see by the file size.
Then you know the contents of a file and the encrypted version. Would that make cracking the encryption feasible? The only solution is a completely encrypted disk with LUKS?