(2) is probably best long term but 1 is easy enough so lets just land that now.

The following revision refers to this bug:
  https://chromium.googlesource.com/chromium/src.git/+/7c0139fc006f41c79976bbbaf68c6cfd5a55020d

commit 7c0139fc006f41c79976bbbaf68c6cfd5a55020d
Author: qyearsley <qyearsley@chromium.org>
Date: Tue Feb 07 22:58:25 2017

In update-test-expectation, skip lines with directories.

BUG= 689642 

Review-Url: https://codereview.chromium.org/2686523003
Cr-Commit-Position: refs/heads/master@{#448765}

[modify] https://crrev.com/7c0139fc006f41c79976bbbaf68c6cfd5a55020d/third_party/WebKit/Tools/Scripts/webkitpy/layout_tests/update_test_expectations.py
[modify] https://crrev.com/7c0139fc006f41c79976bbbaf68c6cfd5a55020d/third_party/WebKit/Tools/Scripts/webkitpy/layout_tests/update_test_expectations_unittest.py

The following revision refers to this bug:
  https://chromium.googlesource.com/chromium/src.git/+/5d73b79a7aff119e64e33a53762910cb40e6d1cc

commit 5d73b79a7aff119e64e33a53762910cb40e6d1cc
Author: qyearsley <qyearsley@chromium.org>
Date: Wed Feb 08 20:27:48 2017

Refactoring: In RemoveFlakesOMatic, use Port.test_isdir.

This is a follow-up to http://crrev.com/2686523003 to make it slightly
simpler; I just noticed that there's already a method for checking
whether a path in the layout tests directory is a directory.

BUG= 689642 

Review-Url: https://codereview.chromium.org/2687683003
Cr-Commit-Position: refs/heads/master@{#449079}

[modify] https://crrev.com/5d73b79a7aff119e64e33a53762910cb40e6d1cc/third_party/WebKit/Tools/Scripts/webkitpy/layout_tests/update_test_expectations.py

Ran the script again to check current behavior, which yielded this change:
https://codereview.chromium.org/2679403004

Since flaky expectations for directories in TestExpectations are relatively rare, I don't think it'll be worth spending more time on this, so I'll mark this as fixed for now.