Removes annotations of "GYP version" from GN targets.

Removes shell.exe.manifest which was used only by the GYP build.

TBR=dpranke@chromium.org

CQ_INCLUDE_TRYBOTS=master.tryserver.chromium.linux:linux_optional_gpu_tests_rel;master.tryserver.chromium.mac:mac_optional_gpu_tests_rel;master.tryserver.chromium.win:win_optional_gpu_tests_rel

Review-Url: https://codereview.chromium.org/2373683003
Cr-Commit-Position: refs/heads/master@{#421335}