cherry-picking fails after making a directory a submodule

[Per Cederqvist <cederp@xxxxxxxxx>]

I have a situation where I have switched a directory from being a
subdirectory to being a submodule.  I then try to cherry-pick a commit
from a taskbranch that was made before the switch to the master
branch.  The commit touches a file outside the subdirectory/submodule.
Yet "git cherry-pick" fails with this error message:

> error: could not apply 78c403e... Add a project feature
> hint: after resolving the conflicts, mark the corrected paths
> hint: with 'git add <paths>' or 'git rm <paths>'
> hint: and commit the result with 'git commit'

I can resolve the situation by running "git add libfoo && git
cherry-pick --continue".  The generated commit contains no changes to
"libfoo".

I don't understand why I need to manually add libfoo, as the commit
I'm cherry-picking doesn't touch anything in libfoo.

The script below can reproduce the issue.  Tested with git 2.15.1,
2.14.0 and 2.8.0, all with the same result.

Is this a bug in "git cherry-pick"?

-- cut here for cherry-across-submodule --
#!/bin/sh
#
# This script creates a simple repo, where the "libfoo" directory
# initially is a normal directory, but later becomes a git submodule.
# It then tries to cherry-pick a commit (that doesn't touch libfoo)
# that was created before the conversion to master (after the
# conversion).  This fails for unclear reasons.

# I've tested this with the following git versions:
#  - 2.8.0
#  - 2.14.0
#  - 2.15.1
#
# They all behave the same

# export PATH=/usr/local/git-2.15.1/bin:$PATH

set -e -x

git --version

# Refuse to run if this directory already exists, to prevent data loss.
mkdir cherry-across-submodule-root
cd cherry-across-submodule-root

mkdir root
(cd root && git init --bare libfoo.git)
(cd root && git init --bare project.git)

mkdir workspace
(cd workspace && git clone ../root/libfoo)
(cd workspace && git clone ../root/project)

proj_commit ()
{
    (cd workspace/project &&
printf "$1\n" >> $2 &&
git add $2 &&
git commit -m"$3")
}

foo_commit ()
{
    (cd workspace/libfoo &&
printf "$1\n" >> $2 &&
git add $2 &&
git commit -m"$3")
}

both_commit ()
{
    foo_commit "$1" $2 "$3"
    proj_commit "$1" libfoo/$2 "Imported libfoo: $3"
}

proj_commit "This is a project" README "Started the project"
mkdir workspace/project/libfoo
both_commit "This is a library" README "Started the library"
both_commit "all:\n\ttouch libfoo.a" Makefile "Build something"
proj_commit "all:\n\tmake -C libfoo" Makefile "Build libfoo"
proj_commit "ceder" AUTHORS "I made this"
both_commit "GPL" "COPYING" "Add license info"
(cd workspace/libfoo && git push)
(cd workspace/project && git push)
(cd workspace/project && git checkout -b task-1)
proj_commit "int feature() { return 17; }" feature.c "Add a project feature"
(cd workspace/project && git push -u origin task-1)

assert_clean()
{
    (cd workspace/project &&
[ -z "`git status --porcelain`" ] )
}

# Cherrypicking task-1 to task-2 works fine.
(cd workspace/project && git checkout -b task-2 master && git
cherry-pick task-1)
assert_clean

(cd workspace/project &&
     git checkout master &&
     git rm -r libfoo &&
     git submodule add -b master ../libfoo.git libfoo &&
     git commit -m"Made libfoo a submodule")
assert_clean


# Now suddenly cherrypicking fails?  I get this message from the
# cherry-pick command:

# error: could not apply 78c403e... Add a project feature
# hint: after resolving the conflicts, mark the corrected paths
# hint: with 'git add <paths>' or 'git rm <paths>'
# hint: and commit the result with 'git commit'

(cd workspace/project && git checkout -b task-3 master && git
cherry-pick task-1)

# At this point, "git status --porcelain" prints two lines:
# A  feature.c
# AU libfoo

assert_clean
-- cut here for cherry-across-submodule --

    /ceder