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Fix bugs related to the latest GN roll.

1) the new GN binary will return an error if you pass it
a file it doesn't know anything about in 'gn refs'.

2) for some reason with the new GN binary we're triggering a
code path in gyp_flag_compare.py that wasn't running before,
and that code path was busted.

TBR=brettw@chromium.org
BUG=
CQ_EXTRA_TRYBOTS=tryserver.chromium.linux:linux_chromium_gn_dbg;tryserver.chromium.mac:mac_chromium_gn_rel,mac_chromium_gn_dbg;tryserver.chromium.win:win8_chromium_gn_rel

Review URL: https://codereview.chromium.org/1109453002

Cr-Commit-Position: refs/heads/master@{#326736}