The other day, in the middle of one of my repositories I found a file. There was something strange about this file: it was a regular file, not a symlink like most of the files in my repository. Maybe it got lost. Maybe I copied it in and forgot to add it. So I tried to add it, but it failed. Or, better, it did not give an error but it also did not change a thing. Why?

$ git-annex add -d Cats.mkv                                                                             
[2019-09-21 12:12:15.243550924] read: git ["--git-dir=../../.git","--work-tree=../..","--literal-pathspecs","symbolic-ref","-q","HEAD"]
[2019-09-21 12:12:15.246431114] process done ExitSuccess
[2019-09-21 12:12:15.246610667] read: git ["--git-dir=../../.git","--work-tree=../..","--literal-pathspecs","show-ref","refs/heads/master"]
[2019-09-21 12:12:15.249072467] process done ExitSuccess
[2019-09-21 12:12:15.249345571] read: git ["--git-dir=../../.git","--work-tree=../..","--literal-pathspecs","ls-files","--others","--exclude-standard","-z","--","Cats & Dogs (2001).mkv"]
[2019-09-21 12:12:15.254996251] read: git ["--git-dir=../../.git","--work-tree=../..","--literal-pathspecs","ls-files","--modified","-z","--","Cats.mkv"]
[2019-09-21 12:12:15.260730984] read: git ["--git-dir=../../.git","--work-tree=../..","--literal-pathspecs","diff","--name-only","--diff-filter=T","-z","--cached","--","Cats.mkv"]

I also found this same file in all clones of this repository! What is going on?

Is it something to do with locked/unlocked files? I never unlock anything. git-annex lock Cats.mkv changes nothing. git-annex list shows no files. git-annex checkpresentkey $(git-annex calckey Cats.mkv) returns error number 1. So, it seems safe to say that the file is not in the repository and it wont't go into the repository (not like this). I find this very puzzling!

Maybe I could use reinject the file into a repository, but I'm trying to diagnose this situation, trying to determine what is going on. However, I'm out of ideas. Any help?