For most files, whether they get annexed is controlled by annex.largefiles. But dotfiles are configured to never be annexed regardless of annex.largefiles. This is unexpected and confusing. More oddly, git-annex-add doesn't seem to add them to regular git, either.

I'm guessing this flows from the new default of git add adding files to the annex, which I hope gets reversed. But separately, I'm not sure why git-annex-add does not add the dotfiles to regular git:

# If you can, paste a complete transcript of the problem occurring here.
# If the problem is with the git-annex assistant, paste in .git/annex/daemon.log

(master_env_v163_py36) 22:32  [newtree02] $ git status
On branch newtree02
Untracked files:
  (use "git add <file>..." to include in what will be committed)

        mydir/

nothing added to commit but untracked files present (use "git add" to track)
(master_env_v163_py36) 22:32  [newtree02] $ ls -al mydir
total 12
drwxrwxr-x 2 ilya ilya 4096 Oct 20 22:31 .
drwxrwxr-x 3 ilya ilya 4096 Oct 20 22:31 ..
-rw-rw-r-- 1 ilya ilya    9 Oct 20 22:31 .mynewdot
(master_env_v163_py36) 22:32  [newtree02] $ git annex add mydir
(master_env_v163_py36) 22:32  [newtree02] $ git status
On branch newtree02
Untracked files:
  (use "git add <file>..." to include in what will be committed)

        mydir/


# End of transcript or log.