Please describe the problem.

If there are staged changes in two files (one in git, one in annex) and I want to commit them by explicitly giving git-commit both paths (in order to exclude other changes that are possibly staged), the not annexed file stays staged, while committing everything staged by not giving any path to git-commit works just fine.

What steps will reproduce the problem?

mkdir testv6
cd testv6
git init
git annex init --version=6
echo some > file_in_git
git -c annex.largefiles=nothing annex add file_in_git
echo more > file_in_annex
git annex add file_in_annex
git commit -m "files added" file_in_git file_in_annex
git status

What version of git-annex are you using? On what operating system?

% git annex version  
git-annex version: 6.20170307+gitg24ade8a25-1~ndall+1
build flags: Assistant Webapp Pairing Testsuite S3(multipartupload)(storageclasses) WebDAV Inotify DBus DesktopNotify ConcurrentOutput TorrentParser MagicMime Feeds Quvi
key/value backends: SHA256E SHA256 SHA512E SHA512 SHA224E SHA224 SHA384E SHA384 SHA3_256E SHA3_256 SHA3_512E SHA3_512 SHA3_224E SHA3_224 SHA3_384E SHA3_384 SKEIN256E SKEIN256 SKEIN512E SKEIN512 SHA1E SHA1 MD5E MD5 WORM URL
remote types: git gcrypt p2p S3 bup directory rsync web bittorrent webdav tahoe glacier ddar hook external
local repository version: 6
supported repository versions: 3 5 6
upgrade supported from repository versions: 0 1 2 3 4 5
operating system: linux x86_64

Please provide any additional information below.

# 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


# End of transcript or log.

Have you had any luck using git-annex before? (Sometimes we get tired of reading bug reports all day and a lil' positive end note does wonders)

ben

done; clean filter defaults to preserving git/annex state of file. --Joey