Goal for today was to make git annex sync --content operate on files hidden by git annex adjust --hide-missing. However, this got into the weeds pretty quickly due to the problem of how to handle --content-of=path when either the whole path or some files within it may be hidden.

Eventually I discovered that git ls-files --with-tree can be used to get a combined list of files in the index plus files in another tree, which in git-annex's case is the original branch that got adjusted. It's not documented to work the way I'm using it (worrying), but it's perfect, because git-annex already uses git ls-files extensively and this could let lots of commands get support for operating on hidden files.

That said, I'm going to limit it to git annex sync for now, because it would be a lot of work to make lots of commands support them, and there could easily be commands where supporting them adds lots of complexity or room for confusion.

Demo time:

joey@darkstar:/tmp> git clone ~/lib/sound/
Cloning into 'sound'...
done.
Checking out files: 100% (45727/45727), done.
joey@darkstar:/tmp> cd sound/
joey@darkstar:/tmp/sound> git annex init --version=6
init  (merging origin/git-annex origin/synced/git-annex into git-annex...)
(scanning for unlocked files...)
ok
joey@darkstar:/tmp/sound> git annex adjust --hide-missing
adjust 
Switched to branch 'adjusted/master(hidemissing)'
ok
joey@darkstar:/tmp/sound#master(hidemissing)> ls
podcasts
joey@darkstar:/tmp/sound#master(hidemissing)> ls podcasts
feeds
joey@darkstar:/tmp/sound#master(hidemissing)> git annex sync origin --no-push -C podcasts
...
joey@darkstar:/tmp/sound> time git annex adjust --hide-missing
adjust
ok
15.03user 3.11system 0:14.95elapsed 121%CPU (0avgtext+0avgdata 93280maxresident)k
0inputs+88outputs (0major+12206minor)pagefaults 0swaps
joey@darkstar:/tmp/sound#master(hidemissing)> ls podcasts
Astronomy_Cast/                                     Hacking_Culture/
Benjamen_Walker_s_Theory_of_Everything/             In_Our_Time/
Clarkesworld_Magazine___Science_Fiction___Fantasy/  Lightspeed_MagazineLightspeed_Magazine___Science_Fiction___Fantasy/
DatCast/                                            Long_Now__Seminars_About_Long_term_Thinking/
Escape_Pod/                                         Love___Radio/
Gravy/                                              feeds

Close to being able to use this on my phone.