git subtree bug produces divergent descendants

[David Ware <davidw@realtimegenomics.com>]

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My group has run into a bug with "git-subtree split". Under some
circumstances a split created from a descendant of another earlier
split is not a descendant of that earlier split (thus blocking
pushes). We originally noticed this on v1.9.1 but have also checked it
on v2.6.3

When scanning the commits to produce the subtree it seems to skip
creating a new commit if any of the parent commits have the same tree
and instead uses that tree in its place. This is fine when the cause
is a branch that did not cause any changes to the subtree.  However it
creates an issue when the cause is both branches ending up with the
same tree through identical alterations (or more likely, one of the
branches has just a subset of the alterations on the other, such as a
branch just containing cherry-picks).

The attached bash script (makerepo.sh) reproduces the problem. To use
create an empty directory and run the script in it. The resulting
'master' branch has had the latest commits on the 'branch' branch
merged into it, so it follows that a subtree on 'folder/' at 'master'
should contain all the commits of a subtree on 'folder/' at 'branch'.
(These subtrees have been produced at 'subtree_tip' and
'subtree_branch' respectively.)

The attached patch (against v2.6.3) fixes the issue for the cases
we've encountered, however since we're not particularly familiar with
git internals we may not have approached this optimally. We suspect it
could be improved to also handle the cases where there are more than 2
parents.

Cheers,
Dave Ware

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From 4bdcd742e5f21d7af57de3e307741efede7d2c6c Mon Sep 17 00:00:00 2001
From: Dave Ware <davidw@netvalue.net.nz>
Date: Fri, 4 Dec 2015 16:30:03 +1300
Subject: [PATCH] Fix bug in git-subtree split.

A bug occurs in 'git-subtree split' where a merge is skipped even when
both parents act on the subtree, provided the merge results in a tree
identical to one of the parents. Fixed by copying the merge if at least
one parent is non-identical, and the non-identical parent is not an
ancestor of the identical parent.
---
 contrib/subtree/git-subtree.sh | 12 ++++++++++--
 1 file changed, 10 insertions(+), 2 deletions(-)

diff --git a/contrib/subtree/git-subtree.sh b/contrib/subtree/git-subtree.sh
index 9f06571..b837531 100755
--- a/contrib/subtree/git-subtree.sh
+++ b/contrib/subtree/git-subtree.sh
@@ -479,8 +479,16 @@ copy_or_skip()
 			p="$p -p $parent"
 		fi
 	done
-	
-	if [ -n "$identical" ]; then
+
+	copycommit=
+	if [ -n "$identical" ] && [ -n "$nonidentical" ]; then
+		extras=$(git rev-list --boundary $identical..$nonidentical)
+		if [ -n "$extras" ]; then
+			# we need to preserve history along the other branch
+			copycommit=1
+		fi
+	fi
+	if [ -n "$identical" ] && [ -z "$copycommit" ]; then
 		echo $identical
 	else
 		copy_commit $rev $tree "$p" || exit $?
-- 
1.9.1