Please describe the problem.

If a submodule is in direct mode, git annex status fails. Apparently the recursive inspection of submodules is done by an internal call to git status, which then misses a working tree in the submodule.

What steps will reproduce the problem?

#!/bin/bash

set -ex
d=$(mktemp -d)
echo "directory: $d"
cd $d
git init
git annex init
echo whatever > file
git annex add file
git commit -m "file added"
mkdir sub
cd sub
git init
git annex init
echo something > subfile
git annex add subfile
git commit -m "subfile added."
cd ..
git submodule add ./sub sub
git commit -m "submodule added"
cd sub
git annex direct
cd ..
git annex status

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

% git annex version
git-annex version: 6.20170209+gitg16be7b5cc-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: unknown
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)

Yes! I think it's a great piece of software!