Clarify that gclient gitmodules' changes need to be committed.

Bug: 1483198
Change-Id: I1dfae06bfc273b01d168b507861984327ad0d629
Reviewed-on: https://chromium-review.googlesource.com/c/chromium/tools/depot_tools/+/4892468
Reviewed-by: Josip Sokcevic <sokcevic@chromium.org>
Commit-Queue: Joanna Wang <jojwang@chromium.org>

gclient.py

@@ -2901,8 +2901,8 @@ def CMDgitmodules(parser, args):
     if cache_info:
         subprocess2.call(['git', 'update-index', '--add'] + cache_info)
     subprocess2.call(['git', 'add', '.gitmodules'])
-    print('.gitmodules and gitlinks updated. Please check git diff and '
+    print('.gitmodules and gitlinks updated. Please check `git diff --staged`'
-          'commit changes.')
+          'and commit those staged changes (`git commit` without -a)')
 
 
 @metrics.collector.collect_metrics('gclient flatten')

presubmit_canned_checks.py

@@ -1963,6 +1963,8 @@ def CheckForCommitObjects(input_api, output_api):
                 'To reset all git submodule git entries to match DEPS, run\n'
                 'the following command in the root of this repository:\n'
                 '    gclient gitmodules'
+                'This will update AND stage the entries to the correct revisions.\n'
+                'Then commit these staged changes only (`git commit` without -a).\n'
                 '\n\n'
                 'The following entries diverged: ' + deps_msg)
         ]