Change clean command to only operate on non-encrypted files as recommended by git docs

[jirutka]

As recommended by gitattributes(5):

For best results, clean should not alter its output further if it is run twice ("clean->clean" should be equivalent to "clean"), and multiple smudge commands should not alter clean's output ("smudge->smudge->clean" should be equivalent to "clean").

I've extracted this change from #107.

Co-Authored-By: @shlomosh

[AGWA]

Does this solve an actual problem? I understand that this is recommended by gitattributes(5), but that man page is thinking of filters that do things like strip carriage returns, which could hypothetically have already been done before committing. Under what circumstances could a file already be encrypted when being committed (that doesn't indicate a deeper problem that needs to be fixed)? I am very hesitant about adding a code path that could cause encryption to be bypassed, so I am seeking to really understand the motivation behind this. Thanks.

[jirutka]

To be honest, I don’t know. I’m just refactoring #107 and this change is not related to the merge command, so I’ve extracted it into a separate PR.