thodg/got

diff --git a/regress/cmdline/add.sh b/regress/cmdline/add.sh
index c77f4d7..030ece4 100755
--- a/regress/cmdline/add.sh
+++ b/regress/cmdline/add.sh
@@ -249,9 +249,57 @@ function test_add_directory {
 	test_done "$testroot" "$ret"
 }
 
+function test_add_clashes_with_submodule {
+	local testroot=`test_init add_clashes_with_submodule`
+
+	make_single_file_repo $testroot/repo2 foo
+
+	(cd $testroot/repo && git submodule -q add ../repo2)
+	(cd $testroot/repo && git commit -q -m 'adding submodule')
+
+	got checkout $testroot/repo $testroot/wt > /dev/null
+
+	# Atttempt to add a file clashes with a submodule
+	echo "This is a file called repo2" > $testroot/wt/repo2
+	(cd $testroot/wt && got add repo2 > /dev/null)
+
+	(cd $testroot/wt && got status > $testroot/stdout)
+	echo "A  repo2" > $testroot/stdout.expected
+	cmp -s $testroot/stdout.expected $testroot/stdout
+	ret="$?"
+	if [ "$ret" != "0" ]; then
+		diff -u $testroot/stdout.expected $testroot/stdout
+		test_done "$testroot" "$ret"
+		return 1
+	fi
+
+	# Update for good measure; see the error below.
+	(cd $testroot/wt && got update > /dev/null)
+
+	# This currently fails with "work tree must be updated"...
+	(cd $testroot/wt && got commit -m 'add file repo2' \
+		> $testroot/stdout 2> $testroot/stderr)
+	ret="$?"
+	if [ "$ret" == "0" ]; then
+		echo "commit succeeded unexpectedly" >&2
+		test_done "$testroot" "1"
+		return 1
+	fi
+
+	echo -n "got: work tree must be updated " > $testroot/stderr.expected
+	echo "before these changes can be committed" >> $testroot/stderr.expected
+	cmp -s $testroot/stderr.expected $testroot/stderr
+	ret="$?"
+	if [ "$ret" != "0" ]; then
+		diff -u $testroot/stderr.expected $testroot/stderr
+	fi
+	test_done "$testroot" "$ret"
+}
+
 run_test test_add_basic
 run_test test_double_add
 run_test test_add_multiple
 run_test test_add_file_in_new_subdir
 run_test test_add_deleted
 run_test test_add_directory
+run_test test_add_clashes_with_submodule
diff --git a/regress/cmdline/blame.sh b/regress/cmdline/blame.sh
index 33d4c77..9e0475a 100755
--- a/regress/cmdline/blame.sh
+++ b/regress/cmdline/blame.sh
@@ -731,6 +731,37 @@ function test_blame_added_on_branch {
 	test_done "$testroot" "$ret"
 }
 
+function test_blame_submodule {
+	local testroot=`test_init blame_submodule`
+	local commit_id0=`git_show_head $testroot/repo`
+	local author_time=`git_show_author_time $testroot/repo`
+
+	make_single_file_repo $testroot/repo2 foo
+
+	(cd $testroot/repo && git submodule -q add ../repo2)
+	(cd $testroot/repo && git commit -q -m 'adding submodule')
+
+	# Attempt a (nonsensical) blame of a submodule.
+	got blame -r $testroot/repo repo2 \
+		> $testroot/stdout 2> $testroot/stderr
+	ret="$?"
+	if [ "$ret" == "0" ]; then
+		echo "blame command succeeded unexpectedly" >&2
+		test_done "$testroot" "1"
+		return 1
+	fi
+	local submodule_id=$(got tree -r $testroot/repo -i | \
+		grep 'repo2\$$' | cut -d ' ' -f1)
+	echo "got: object $submodule_id not found" > $testroot/stderr.expected
+
+	cmp -s $testroot/stderr.expected $testroot/stderr
+	ret="$?"
+	if [ "$ret" != "0" ]; then
+		diff -u $testroot/stderr.expected $testroot/stderr
+	fi
+	test_done "$testroot" "$ret"
+}
+
 run_test test_blame_basic
 run_test test_blame_tag
 run_test test_blame_file_single_line
@@ -741,3 +772,4 @@ run_test test_blame_lines_shifted_down
 run_test test_blame_commit_subsumed
 run_test test_blame_blame_h
 run_test test_blame_added_on_branch
+run_test test_blame_submodule
diff --git a/regress/cmdline/cat.sh b/regress/cmdline/cat.sh
index e94f002..3c88697 100755
--- a/regress/cmdline/cat.sh
+++ b/regress/cmdline/cat.sh
@@ -202,5 +202,64 @@ function test_cat_path {
 	test_done "$testroot" "$ret"
 }
 
+function test_cat_submodule {
+	local testroot=`test_init cat_submodule`
+
+	make_single_file_repo $testroot/repo2 foo
+
+	(cd $testroot/repo && git submodule -q add ../repo2)
+	(cd $testroot/repo && git commit -q -m 'adding submodule')
+
+	got cat -r $testroot/repo repo2 > $testroot/stdout \
+		> $testroot/stdout 2> $testroot/stderr
+	ret="$?"
+	if [ "$ret" == "0" ]; then
+		echo "cat command succeeded unexpectedly" >&2
+		test_done "$testroot" "1"
+		return 1
+	fi
+	local submodule_id=$(got tree -r $testroot/repo -i | \
+		grep 'repo2\$$' | cut -d ' ' -f1)
+	echo "got: object $submodule_id not found" > $testroot/stderr.expected
+
+	cmp -s $testroot/stderr.expected $testroot/stderr
+	ret="$?"
+	if [ "$ret" != "0" ]; then
+		diff -u $testroot/stderr.expected $testroot/stderr
+	fi
+	test_done "$testroot" "$ret"
+}
+
+function test_cat_submodule_of_same_repo {
+	local testroot=`test_init cat_submodule_of_same_repo`
+	local commit_id0=`git_show_head $testroot/repo`
+	local author_time=`git_show_author_time $testroot/repo`
+
+	(cd $testroot && git clone -q repo repo2 >/dev/null)
+	(cd $testroot/repo && git submodule -q add ../repo2)
+	(cd $testroot/repo && git commit -q -m 'adding submodule')
+
+	# 'got cat' shows the commit object which the submodule points to
+	# because a commit with the same ID exists in the outer repository
+	got cat -r $testroot/repo $commit_id0 | grep ^tree > $testroot/stdout.expected
+	echo "numparents 0" >> $testroot/stdout.expected
+	echo "author $GOT_AUTHOR $author_time +0000" >> $testroot/stdout.expected
+	echo "committer $GOT_AUTHOR $author_time +0000" \
+		>> $testroot/stdout.expected
+	echo "messagelen 22" >> $testroot/stdout.expected
+	printf "\nadding the test tree\n" >> $testroot/stdout.expected
+
+	got cat -r $testroot/repo repo2 > $testroot/stdout
+	cmp -s $testroot/stdout.expected $testroot/stdout
+	ret="$?"
+	if [ "$ret" != "0" ]; then
+		diff -u $testroot/stdout.expected $testroot/stdout
+	fi
+
+	test_done "$testroot" "$ret"
+}
+
 run_test test_cat_basic
 run_test test_cat_path
+run_test test_cat_submodule
+run_test test_cat_submodule_of_same_repo
diff --git a/regress/cmdline/checkout.sh b/regress/cmdline/checkout.sh
index 6d3a99a..abba81a 100755
--- a/regress/cmdline/checkout.sh
+++ b/regress/cmdline/checkout.sh
@@ -261,7 +261,8 @@ function test_checkout_tag {
 function test_checkout_ignores_submodules {
 	local testroot=`test_init checkout_ignores_submodules`
 
-	(cd $testroot && git clone -q repo repo2 >/dev/null)
+	make_single_file_repo $testroot/repo2 foo
+
 	(cd $testroot/repo && git submodule -q add ../repo2)
 	(cd $testroot/repo && git commit -q -m 'adding submodule')
 
diff --git a/regress/cmdline/cherrypick.sh b/regress/cmdline/cherrypick.sh
index 8cca1c7..1536606 100755
--- a/regress/cmdline/cherrypick.sh
+++ b/regress/cmdline/cherrypick.sh
@@ -234,6 +234,120 @@ function test_cherrypick_into_work_tree_with_conflicts {
 	test_done "$testroot" "$ret"
 }
 
+function test_cherrypick_modified_submodule {
+	local testroot=`test_init cherrypick_modified_submodules`
+
+	make_single_file_repo $testroot/repo2 foo
+
+	(cd $testroot/repo && git submodule -q add ../repo2)
+	(cd $testroot/repo && git commit -q -m 'adding submodule')
+
+	got checkout $testroot/repo $testroot/wt > /dev/null
+
+	echo "modified foo" > $testroot/repo2/foo
+	(cd $testroot/repo2 && git commit -q -a -m 'modified a submodule')
+
+	(cd $testroot/repo && git checkout -q -b newbranch)
+	# Update the repo/repo2 submodule link on newbranch
+	(cd $testroot/repo && git -C repo2 pull -q)
+	(cd $testroot/repo && git add repo2)
+	git_commit $testroot/repo -m "modified submodule link"
+	local commit_id=`git_show_head $testroot/repo`
+
+	# This cherrypick is a no-op because Got's file index
+	# does not track submodules.
+	(cd $testroot/wt && got cherrypick $commit_id > $testroot/stdout)
+
+	echo -n > $testroot/stdout.expected
+	cmp -s $testroot/stdout.expected $testroot/stdout
+	ret="$?"
+	if [ "$ret" != "0" ]; then
+		diff -u $testroot/stdout.expected $testroot/stdout
+	fi
+	test_done "$testroot" "$ret"
+}
+
+function test_cherrypick_added_submodule {
+	local testroot=`test_init cherrypick_added_submodules`
+
+	got checkout $testroot/repo $testroot/wt > /dev/null
+
+	make_single_file_repo $testroot/repo2 foo
+
+	# Add the repo/repo2 submodule on newbranch
+	(cd $testroot/repo && git checkout -q -b newbranch)
+	(cd $testroot/repo && git submodule -q add ../repo2)
+	(cd $testroot/repo && git commit -q -m 'adding submodule')
+	local commit_id=`git_show_head $testroot/repo`
+
+	(cd $testroot/wt && got cherrypick $commit_id > $testroot/stdout)
+
+	echo "A  .gitmodules" > $testroot/stdout.expected
+	echo "Merged commit $commit_id" >> $testroot/stdout.expected
+	cmp -s $testroot/stdout.expected $testroot/stdout
+	ret="$?"
+	if [ "$ret" != "0" ]; then
+		diff -u $testroot/stdout.expected $testroot/stdout
+	fi
+	test_done "$testroot" "$ret"
+}
+
+function test_cherrypick_conflict_wt_file_vs_repo_submodule {
+	local testroot=`test_init cherrypick_conflict_wt_file_vs_repo_submodule`
+
+	got checkout $testroot/repo $testroot/wt > /dev/null
+
+	# Add a file which will clash with the submodule
+	echo "This is a file called repo2" > $testroot/wt/repo2
+	(cd $testroot/wt && got add repo2 > /dev/null)
+	(cd $testroot/wt && got commit -m 'add file repo2' > /dev/null)
+	ret="$?"
+	if [ "$ret" != "0" ]; then
+		echo "commit failed unexpectedly" >&2
+		test_done "$testroot" "1"
+		return 1
+	fi
+
+	make_single_file_repo $testroot/repo2 foo
+
+	# Add the repo/repo2 submodule on newbranch
+	(cd $testroot/repo && git checkout -q -b newbranch)
+	(cd $testroot/repo && git submodule -q add ../repo2)
+	(cd $testroot/repo && git commit -q -m 'adding submodule')
+	local commit_id=`git_show_head $testroot/repo`
+
+	# Modify the clashing file such that any modifications brought
+	# in by 'got cherrypick' would require a merge.
+	echo "This file was changed" > $testroot/wt/repo2
+
+	(cd $testroot/wt && got update >/dev/null)
+	(cd $testroot/wt && got cherrypick $commit_id > $testroot/stdout)
+
+	echo "A  .gitmodules" > $testroot/stdout.expected
+	echo "Merged commit $commit_id" >> $testroot/stdout.expected
+	cmp -s $testroot/stdout.expected $testroot/stdout
+	ret="$?"
+	if [ "$ret" != "0" ]; then
+		diff -u $testroot/stdout.expected $testroot/stdout
+		test_done "$testroot" "$ret"
+		return 1
+	fi
+
+	(cd $testroot/wt && got status > $testroot/stdout)
+
+	echo "A  .gitmodules" > $testroot/stdout.expected
+	echo "M  repo2" >> $testroot/stdout.expected
+	cmp -s $testroot/stdout.expected $testroot/stdout
+	ret="$?"
+	if [ "$ret" != "0" ]; then
+		diff -u $testroot/stdout.expected $testroot/stdout
+	fi
+	test_done "$testroot" "$ret"
+}
+
 run_test test_cherrypick_basic
 run_test test_cherrypick_root_commit
 run_test test_cherrypick_into_work_tree_with_conflicts
+run_test test_cherrypick_modified_submodule
+run_test test_cherrypick_added_submodule
+run_test test_cherrypick_conflict_wt_file_vs_repo_submodule
diff --git a/regress/cmdline/commit.sh b/regress/cmdline/commit.sh
index aafe145..3c8e833 100755
--- a/regress/cmdline/commit.sh
+++ b/regress/cmdline/commit.sh
@@ -862,6 +862,43 @@ function test_commit_normalizes_filemodes {
 	test_done "$testroot" "$ret"
 }
 
+function test_commit_with_unrelated_submodule {
+	local testroot=`test_init commit_with_unrelated_submodule`
+
+	make_single_file_repo $testroot/repo2 foo
+
+	(cd $testroot/repo && git submodule -q add ../repo2)
+	(cd $testroot/repo && git commit -q -m 'adding submodule')
+
+	got checkout $testroot/repo $testroot/wt > /dev/null
+	ret="$?"
+	if [ "$ret" != "0" ]; then
+		test_done "$testroot" "$ret"
+		return 1
+	fi
+
+	echo "modified alpha" > $testroot/wt/alpha
+
+	# Currently fails with "bad file type" error
+	(cd $testroot/wt && got commit -m 'modify alpha' \
+		> $testroot/stdout 2> $testroot/stderr)
+	ret="$?"
+	if [ "$ret" == "0" ]; then
+		echo "commit succeeded unexpectedly" >&2
+		test_done "$testroot" "1"
+		return 1
+	fi
+	echo "got: bad file type" > $testroot/stderr.expected
+
+	cmp -s $testroot/stderr.expected $testroot/stderr
+	ret="$?"
+	if [ "$ret" != "0" ]; then
+		diff -u $testroot/stderr.expected $testroot/stderr
+		return 1
+	fi
+	test_done "$testroot" "$ret"
+}
+
 run_test test_commit_basic
 run_test test_commit_new_subdir
 run_test test_commit_subdir
@@ -881,3 +918,4 @@ run_test test_commit_tree_entry_sorting
 run_test test_commit_gitconfig_author
 run_test test_commit_xbit_change
 run_test test_commit_normalizes_filemodes
+run_test test_commit_with_unrelated_submodule
diff --git a/regress/cmdline/common.sh b/regress/cmdline/common.sh
index ff453b2..5104375 100644
--- a/regress/cmdline/common.sh
+++ b/regress/cmdline/common.sh
@@ -129,6 +129,27 @@ function make_test_tree
 	echo zeta > $repo/epsilon/zeta
 }
 
+function make_single_file_repo
+{
+	repo="$1"
+	file="$2"
+
+	mkdir $repo
+	git_init $repo
+	echo "this is file $file" > $repo/$file
+	(cd $repo && git add .)
+	git_commit $repo -m "intialize $repo with file $file"
+}
+
+function get_loose_object_path
+{
+	local repo="$1"
+	local id="$2"
+	local id0=`trim_obj_id 38 $id`
+	local idrest=`echo ${id#[0-9a-f][0-9a-f]}`
+	echo "$repo/.git/objects/$id0/$idrest"
+}
+
 function get_blob_id
 {
 	repo="$1"
diff --git a/regress/cmdline/diff.sh b/regress/cmdline/diff.sh
index 6fb2ea6..a3f99c8 100755
--- a/regress/cmdline/diff.sh
+++ b/regress/cmdline/diff.sh
@@ -329,8 +329,42 @@ function test_diff_ignore_whitespace {
 	test_done "$testroot" "$ret"
 }
 
+function test_diff_submodule_of_same_repo {
+	local testroot=`test_init diff_submodule_of_same_repo`
+
+	(cd $testroot && git clone -q repo repo2 >/dev/null)
+	(cd $testroot/repo && git submodule -q add ../repo2)
+	(cd $testroot/repo && git commit -q -m 'adding submodule')
+
+	epsilon_id=$(got tree -r $testroot/repo -i | grep 'epsilon/$' | \
+		cut -d ' ' -f 1)
+	submodule_id=$(got tree -r $testroot/repo -i | grep 'repo2\$$' | \
+		cut -d ' ' -f 1)
+
+	# Attempt a (nonsensical) diff between a tree object and a submodule.
+	# Currently fails with "wrong type of object" error
+	got diff -r $testroot/repo $epsilon_id $submodule_id \
+		> $testroot/stdout 2> $testroot/stderr
+	ret="$?"
+	if [ "$ret" == "0" ]; then
+		echo "diff command succeeded unexpectedly" >&2
+		test_done "$testroot" "1"
+		return 1
+	fi
+	echo "got: wrong type of object" > $testroot/stderr.expected
+
+	cmp -s $testroot/stderr.expected $testroot/stderr
+	ret="$?"
+	if [ "$ret" != "0" ]; then
+		diff -u $testroot/stderr.expected $testroot/stderr
+		return 1
+	fi
+	test_done "$testroot" "$ret"
+}
+
 run_test test_diff_basic
 run_test test_diff_shows_conflict
 run_test test_diff_tag
 run_test test_diff_lightweight_tag
 run_test test_diff_ignore_whitespace
+run_test test_diff_submodule_of_same_repo
diff --git a/regress/cmdline/log.sh b/regress/cmdline/log.sh
index d88d0fa..c563ee1 100755
--- a/regress/cmdline/log.sh
+++ b/regress/cmdline/log.sh
@@ -690,6 +690,85 @@ function test_log_changed_paths {
 	test_done "$testroot" "$ret"
 }
 
+function test_log_submodule {
+	local testroot=`test_init log_submodule`
+
+	make_single_file_repo $testroot/repo2 foo
+
+	(cd $testroot/repo && git submodule -q add ../repo2)
+	(cd $testroot/repo && git commit -q -m 'adding submodule')
+	local head_commit=`git_show_head $testroot/repo`
+
+	echo "commit $head_commit (master)" > $testroot/stdout.expected
+
+	got log -r $testroot/repo -l1 repo2 | grep ^commit > $testroot/stdout
+	cmp -s $testroot/stdout.expected $testroot/stdout
+	ret="$?"
+	if [ "$ret" != "0" ]; then
+		diff -u $testroot/stdout.expected $testroot/stdout
+		test_done "$testroot" "$ret"
+		return 1
+	fi
+
+	echo " A  .gitmodules" > $testroot/stdout.expected
+
+	got log -r $testroot/repo -l1 -P repo2 | grep '^ [MDmA]' \
+		> $testroot/stdout
+	cmp -s $testroot/stdout.expected $testroot/stdout
+	ret="$?"
+	if [ "$ret" != "0" ]; then
+		diff -u $testroot/stdout.expected $testroot/stdout
+		test_done "$testroot" "$ret"
+		return 1
+	fi
+
+	got log -p -r $testroot/repo -l1 repo2 \
+		> $testroot/stdout 2> $testroot/stderr
+	ret="$?"
+	if [ "$ret" == "0" ]; then
+		echo "log command succeeded unexpectedly" >&2
+		test_done "$testroot" "1"
+		return 1
+	fi
+	local submodule_id=$(got tree -r $testroot/repo -i | \
+		grep 'repo2\$$' | cut -d ' ' -f1)
+	echo "got: object $submodule_id not found" > $testroot/stderr.expected
+
+	cmp -s $testroot/stderr.expected $testroot/stderr
+	ret="$?"
+	if [ "$ret" != "0" ]; then
+		diff -u $testroot/stderr.expected $testroot/stderr
+		test_done "$testroot" "$ret"
+		return 1
+	fi
+
+	echo "modified foo" > $testroot/repo2/foo
+	(cd $testroot/repo2 && git commit -q -a -m 'modified a submodule')
+
+	# Update the repo/repo2 submodule link
+	(cd $testroot/repo && git -C repo2 pull -q)
+	(cd $testroot/repo && git add repo2)
+	git_commit $testroot/repo -m "changed submodule link"
+
+	# log -P does not show the changed submodule path
+	got log -P -r $testroot/repo -l1 repo2 > $testroot/stdout.full
+	ret="$?"
+	if [ "$ret" != "0" ]; then
+		echo "log command failed unexpectedly" >&2
+		test_done "$testroot" "1"
+		return 1
+	fi
+	grep '^ [MDmA]' $testroot/stdout.full > $testroot/stdout
+
+	echo -n > $testroot/stdout.expected
+	cmp -s $testroot/stdout.expected $testroot/stdout
+	ret="$?"
+	if [ "$ret" != "0" ]; then
+		diff -u $testroot/stdout.expected $testroot/stdout
+	fi
+	test_done "$testroot" "$ret"
+}
+
 run_test test_log_in_repo
 run_test test_log_in_bare_repo
 run_test test_log_in_worktree
@@ -702,3 +781,4 @@ run_test test_log_end_at_commit
 run_test test_log_reverse_display
 run_test test_log_in_worktree_different_repo
 run_test test_log_changed_paths
+run_test test_log_submodule
diff --git a/regress/cmdline/tree.sh b/regress/cmdline/tree.sh
index 5a9d63d..44be74f 100755
--- a/regress/cmdline/tree.sh
+++ b/regress/cmdline/tree.sh
@@ -77,5 +77,65 @@ function test_tree_branch {
 	test_done "$testroot" "$ret"
 }
 
+function test_tree_submodule {
+	local testroot=`test_init tree_submodule`
+
+	make_single_file_repo $testroot/repo2 foo
+	(cd $testroot/repo && git submodule -q add ../repo2)
+	(cd $testroot/repo && git commit -q -m 'adding submodule')
+
+	local submodule_id=$(got tree -r $testroot/repo -i | \
+		grep 'repo2\$$' | cut -d ' ' -f1)
+	local objpath=`get_loose_object_path $testroot/repo $submodule_id`
+
+	# Currently fails in open(2)
+	got tree -r $testroot/repo repo2 > $testroot/stdout 2> $testroot/stderr
+	ret="$?"
+	if [ "$ret" == "0" ]; then
+		echo "tree command succeeded unexpectedly" >&2
+		test_done "$testroot" "1"
+		return 1
+	fi
+	echo "got: open: $objpath: No such file or directory" \
+		> $testroot/stderr.expected
+
+	cmp -s $testroot/stderr.expected $testroot/stderr
+	ret="$?"
+	if [ "$ret" != "0" ]; then
+		diff -u $testroot/stderr.expected $testroot/stderr
+		return 1
+	fi
+	test_done "$testroot" "$ret"
+}
+
+function test_tree_submodule_of_same_repo {
+	local testroot=`test_init tree_submodule_of_same_repo`
+
+	(cd $testroot && git clone -q repo repo2 >/dev/null)
+	(cd $testroot/repo && git submodule -q add ../repo2)
+	(cd $testroot/repo && git commit -q -m 'adding submodule')
+
+	# Currently fails with "bad object data"
+	got tree -r $testroot/repo repo2 > $testroot/stdout 2> $testroot/stderr
+	ret="$?"
+	if [ "$ret" == "0" ]; then
+		echo "tree command succeeded unexpectedly" >&2
+		test_done "$testroot" "1"
+		return 1
+	fi
+	echo "got-read-tree: bad object data" > $testroot/stderr.expected
+	echo "got: bad object data" >> $testroot/stderr.expected
+
+	cmp -s $testroot/stderr.expected $testroot/stderr
+	ret="$?"
+	if [ "$ret" != "0" ]; then
+		diff -u $testroot/stderr.expected $testroot/stderr
+		return 1
+	fi
+	test_done "$testroot" "$ret"
+}
+
 run_test test_tree_basic
 run_test test_tree_branch
+run_test test_tree_submodule
+run_test test_tree_submodule_of_same_repo
diff --git a/regress/cmdline/update.sh b/regress/cmdline/update.sh
index 05fd291..60a1a2a 100755
--- a/regress/cmdline/update.sh
+++ b/regress/cmdline/update.sh
@@ -1710,6 +1710,122 @@ function test_update_preserves_conflicted_file {
 	test_done "$testroot" "$ret"
 }
 
+function test_update_modified_submodules {
+	local testroot=`test_init update_modified_submodules`
+
+	make_single_file_repo $testroot/repo2 foo
+
+	(cd $testroot/repo && git submodule -q add ../repo2)
+	(cd $testroot/repo && git commit -q -m 'adding submodule')
+
+	got checkout $testroot/repo $testroot/wt > /dev/null
+
+	echo "modified foo" > $testroot/repo2/foo
+	(cd $testroot/repo2 && git commit -q -a -m 'modified a submodule')
+
+	# Update the repo/repo2 submodule link
+	(cd $testroot/repo && git -C repo2 pull -q)
+	(cd $testroot/repo && git add repo2)
+	git_commit $testroot/repo -m "modified submodule link"
+
+	# This update only records the new base commit. Otherwise it is a
+	# no-op change because Got's file index does not track submodules.
+	echo -n "Updated to commit " > $testroot/stdout.expected
+	git_show_head $testroot/repo >> $testroot/stdout.expected
+	echo >> $testroot/stdout.expected
+
+	(cd $testroot/wt && got update > $testroot/stdout)
+
+	cmp -s $testroot/stdout.expected $testroot/stdout
+	ret="$?"
+	if [ "$ret" != "0" ]; then
+		diff -u $testroot/stdout.expected $testroot/stdout
+	fi
+	test_done "$testroot" "$ret"
+}
+
+function test_update_adds_submodule {
+	local testroot=`test_init update_adds_submodule`
+
+	got checkout $testroot/repo $testroot/wt > /dev/null
+
+	make_single_file_repo $testroot/repo2 foo
+
+	echo "modified foo" > $testroot/repo2/foo
+	(cd $testroot/repo2 && git commit -q -a -m 'modified a submodule')
+
+	(cd $testroot/repo && git submodule -q add ../repo2)
+	(cd $testroot/repo && git commit -q -m 'adding submodule')
+
+	echo "A  .gitmodules" > $testroot/stdout.expected
+	echo -n "Updated to commit " >> $testroot/stdout.expected
+	git_show_head $testroot/repo >> $testroot/stdout.expected
+	echo >> $testroot/stdout.expected
+
+	(cd $testroot/wt && got update > $testroot/stdout)
+
+	cmp -s $testroot/stdout.expected $testroot/stdout
+	ret="$?"
+	if [ "$ret" != "0" ]; then
+		diff -u $testroot/stdout.expected $testroot/stdout
+	fi
+	test_done "$testroot" "$ret"
+}
+
+function test_update_conflict_wt_file_vs_repo_submodule {
+	local testroot=`test_init update_conflict_wt_file_vs_repo_submodule`
+
+	got checkout $testroot/repo $testroot/wt > /dev/null
+
+	make_single_file_repo $testroot/repo2 foo
+
+	# Add a file which will clash with the submodule
+	echo "This is a file called repo2" > $testroot/wt/repo2
+	(cd $testroot/wt && got add repo2 > /dev/null)
+	(cd $testroot/wt && got commit -m 'add file repo2' > /dev/null)
+	ret="$?"
+	if [ "$ret" != "0" ]; then
+		echo "commit failed unexpectedly" >&2
+		test_done "$testroot" "1"
+		return 1
+	fi
+
+	(cd $testroot/repo && git submodule -q add ../repo2)
+	(cd $testroot/repo && git commit -q -m 'adding submodule')
+
+	# Modify the clashing file such that any modifications brought
+	# in by 'got update' would require a merge.
+	echo "This file was changed" > $testroot/wt/repo2
+
+	# No conflict occurs because 'got update' ignores the submodule
+	# and leaves the clashing file as it was.
+	echo "A  .gitmodules" > $testroot/stdout.expected
+	echo -n "Updated to commit " >> $testroot/stdout.expected
+	git_show_head $testroot/repo >> $testroot/stdout.expected
+	echo >> $testroot/stdout.expected
+
+	(cd $testroot/wt && got update > $testroot/stdout)
+
+	cmp -s $testroot/stdout.expected $testroot/stdout
+	ret="$?"
+	if [ "$ret" != "0" ]; then
+		diff -u $testroot/stdout.expected $testroot/stdout
+		test_done "$testroot" "$ret"
+		return 1
+	fi
+
+	(cd $testroot/wt && got status > $testroot/stdout)
+
+	echo "M  repo2" > $testroot/stdout.expected
+	cmp -s $testroot/stdout.expected $testroot/stdout
+	ret="$?"
+	if [ "$ret" != "0" ]; then
+		diff -u $testroot/stdout.expected $testroot/stdout
+	fi
+	test_done "$testroot" "$ret"
+}
+
+
 run_test test_update_basic
 run_test test_update_adds_file
 run_test test_update_deletes_file
@@ -1742,3 +1858,6 @@ run_test test_update_bumps_base_commit_id
 run_test test_update_tag
 run_test test_update_toggles_xbit
 run_test test_update_preserves_conflicted_file
+run_test test_update_modified_submodules
+run_test test_update_adds_submodule
+run_test test_update_conflict_wt_file_vs_repo_submodule