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.

There have been several changes to dotfiles since this bug was filed. I think most relevantly, annex.dotfiles can be set to let annex.largefiles control them too. So this seems done --Joey