[[!comment format=mdwn
 username="kyle"
 avatar="http://cdn.libravatar.org/avatar/7d6e85cde1422ad60607c87fa87c63f3"
 subject="comment 4"
 date="2020-08-20T20:34:23Z"
 content="""
Git tracks the symlink.  After your first commit, here's what is
tracked for protein/milk:

```
$ git show HEAD:protein/milk
../.git/annex/objects/M4/kf/SHA256E-s5--ccfd6ff816d055a64ff4421370d71bc5cdb2a1e0a8afa62b69bb52dd0781f00c/SHA256E-s5--ccfd6ff816d055a64ff4421370d71bc5cdb2a1e0a8afa62b69bb52dd0781f00c
```

And after your second commit:

```
$ git show HEAD:amino-acids/milk
../.git/annex/objects/M4/kf/SHA256E-s5--ccfd6ff816d055a64ff4421370d71bc5cdb2a1e0a8afa62b69bb52dd0781f00c/SHA256E-s5--ccfd6ff816d055a64ff4421370d71bc5cdb2a1e0a8afa62b69bb52dd0781f00c
```

Note that it's exactly the same content, and Git will (by default)
present it as a rename.

In your final commit, the link that Git tracks changes:

```
$ git show HEAD:atoms
.git/annex/objects/M4/kf/SHA256E-s5--ccfd6ff816d055a64ff4421370d71bc5cdb2a1e0a8afa62b69bb52dd0781f00c/SHA256E-s5--ccfd6ff816d055a64ff4421370d71bc5cdb2a1e0a8afa62b69bb52dd0781f00c
```

Notice that the leading part of the link changed, corresponding to the
movement out of the subdirectory.

"""]]
