[scm] Remove gitlinks from list of affected files

Presubmit checks expect files to be actual files. Gitlink entries are
directories (if initialized), and that breaks various existing tests.

Since we don't run presubmits from git dependencies, it's safe to ignore
any updates to gitlinks and omit them from All Files.

R=jojwang

Change-Id: I670e5caef4067a0203578e9be50c4fabf23b3153
Reviewed-on: https://chromium-review.googlesource.com/c/chromium/tools/depot_tools/+/4795116
Auto-Submit: Josip Sokcevic <sokcevic@chromium.org>
Commit-Queue: Joanna Wang <jojwang@chromium.org>
Reviewed-by: Joanna Wang <jojwang@chromium.org>

scm.py

@@ -132,7 +132,7 @@ class GIT(object):
         raise gclient_utils.Error('Cannot determine upstream branch')
     command = [
         '-c', 'core.quotePath=false', 'diff', '--name-status', '--no-renames',
-        '-r',
+        '--ignore-submodules=all', '-r',
         '%s...%s' % (upstream_branch, end_commit)
     ]
     status = GIT.Capture(command, cwd)
@@ -382,8 +382,10 @@ class GIT(object):
   @staticmethod
   def GetAllFiles(cwd):
     """Returns the list of all files under revision control."""
-    command = ['-c', 'core.quotePath=false', 'ls-files', '--', '.']
-    return GIT.Capture(command, cwd=cwd).splitlines(False)
+    command = ['-c', 'core.quotePath=false', 'ls-files', '-s', '--', '.']
+    files = GIT.Capture(command, cwd=cwd).splitlines(False)
+    # return only files
+    return [f.split(maxsplit=4)[-1] for f in files if f.startswith('100')]
 
   @staticmethod
   def GetPatchName(cwd):