On Tue, Dec 15, 2015 at 09:17:30PM -0600, David A. Greene wrote:
> According to the rebase man page, rebase gathers commits as in "git log
> <upstream>..HEAD."  However, that is not what happens in the tests
> below.  Some of the commits disappear.
> 
> The test basically does this:
> 
> - Setup a master project and a subproject, merged via a subtree-like
>   merge (this is how git-subtree does it).
> 
> - Add some commits to the subproject directory after the subtree merge,
>   to create some history not in the original subproject.
> 
> - filter-branch --subdirectory-filter to extract commits from the
>   subproject directory.
> 
> - Rebase those commits back on to the original subproject repository.
> 
> The above loses all commits made after the subproject is merged into
> the main project.
[snip]
> # Does not preserve master4 and master5.
> test_expect_success 'Rebase default' '
>       git checkout -b rebase-default master &&
>       git filter-branch --prune-empty -f --subdirectory-filter files_subtree 
> &&
>       git commit -m "Empty commit" --allow-empty &&
>       git rebase -Xsubtree=files_subtree  --preserve-merges --onto 
> files-master master &&

It seems that the problem is introduces by --preserve-merges (and
-Xsubtree causes something interesting to happen as well).  I see the
following behaviour:

git rebase --onto files-master master

        Works (master4 and master5 preserved).

git rebase --preserve-merges --onto files-master master

        Behaves as described above (master4 and master5 are lost).

git rebase -Xsubtree=files_subtree --onto files-master master

        fatal: Could not parse object 
'b15c4133fc3146e1330c84159886f0f7a09fbf43^'
        Unknown exit code (128) from command: git-merge-recursive 
b15c4133fc3146e1330c84159886f0f7a09fbf43^ -- HEAD 
b15c4133fc3146e1330c84159886f0f7a09fbf43 

git rebase -Xsubtree=files_subtree --preserve-merges --onto files-master master

        Same as the version with only --preserve-merges.
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