Merge pull request #1239 from ethomson/index_remove

add an index_remove_bypath that removes conflicts

diff --cc src/submodule.c
Simple merge

diff --cc tests-clar/checkout/index.c
Simple merge

diff --cc tests-clar/checkout/tree.c
index b877b2eca69ac809c809b2f7d8d8f93344c8dcf7,176dcceb9450b55827e9a09e6b514eb82edd1672..821cbfe0e48e1313fded69c0b64478649e09a26d
--- 1/tests-clar/checkout/tree.c
--- 2/tests-clar/checkout/tree.c
+++ b/tests-clar/checkout/tree.c
@@@ -407,9 -406,8 +407,9 @@@ void assert_conflict
                GIT_EMERGECONFLICT, git_checkout_tree(g_repo, g_object, &g_opts));
  
        /* Stage the conflicting change */
-       cl_git_pass(git_index_add_from_workdir(index, entry_path));
+       cl_git_pass(git_index_add_bypath(index, entry_path));
        cl_git_pass(git_index_write(index));
 +      git_index_free(index);
  
        cl_assert_equal_i(
                GIT_EMERGECONFLICT, git_checkout_tree(g_repo, g_object, &g_opts));