I am just beginning to use git-annex so it is possible that the following issue was caused by my own mistake. It cropped up after commiting a number of files that had been moved between subfolders, and added with git add -A etc.

When files are locked, I am able to view their contents. However, when I unlock certain files, their contents appear to be replaced by the contents of the symlink. Locking them again allows me to view their contents. For instance, with one unlocked file, say test.md, I get

$ cat test.md

Some files still behave as expected.

My git-annex repo is in my Linux home folder on an ext4 partition. My repo uses git-annex version 6.

I did have a look at this discussion but none of the solutions there seemed to do the trick.

Any help is much appreciated.