directory / submodule merge conflcts

[Mark Levedahl <mlevedahl@verizon.net>]

Over time, I have converted a number of subdirectories in a main project 
into submodules, while maintaining the complete pathnames intact. Thus, 
only git knows that an object at code/dir1 is a submodule or a 
subdirectory of the superproject.

git has trouble merging branches across the above boundaries, the script 
below demonstrates the issue. I cannot merge the main branch and a 
branch that occurred before conversion to a submodule.

Paraphrasing the script, the formula is
    - create a superproject with a subdirectory (sub1)
    - on master, convert sub1 to a submodule (no other changes)
    - on branch base (before sub1 conversion to a submodule), change a 
file not in sub1 (no other changes)
    - merge master into base - failure

The actual reported error message is:
fatal: cannot read object b500f4d0c6aaf40a0251da35b82c0fa5c57b6503 
'sub1~master': It is a submodule!
Merge with strategy recursive failed.

Any ideas or hints on how to improve this would be greatly appreciated.

Thanks,
Mark

#!/bin/sh
#
# demonstrate issue with directory / submodule (D/S) conflict problem

mkdir dsprob || exit
cd dsprob
git init
mkdir sub1
echo hi > foo
echo hi1 > sub1/foo
git add .
git commit -m "Create base"
git checkout -b base
echo bye >> foo
git add .
git commit -m "Modify base"
git checkout master

# make sub1 a submodule
git rm -r -f sub1
git commit -m "removed sub1 directory"
git checkout base sub1
git reset
cd sub1
git init
git add .
git commit -m "Start sub1 as its own project"
cd ..
mv sub1 sub1_repo
git submodule add "$(pwd)/sub1_repo" sub1
git commit -m "Added sub1 as a submodule"

# now, go back to base and try to merge
rm -rf sub1
git checkout -f base
git merge master