Fix bootstrap.py

Generate cfi_flags buildflags header in bootstrap.py and add comments to
base/BUILD.gn to try to prevent regressions.

Change-Id: I3da0817b4880d3f0ba732ead0a53d1b708258da8
Reviewed-on: https://chromium-review.googlesource.com/728379
Reviewed-by: Dirk Pranke <dpranke@chromium.org>
Reviewed-by: Nico Weber <thakis@chromium.org>
Commit-Queue: Peter Collingbourne <pcc@chromium.org>
Cr-Original-Commit-Position: refs/heads/master@{#510552}
Cr-Mirrored-From: https://chromium.googlesource.com/chromium/src
Cr-Mirrored-Commit: 29b1eb6e480f2fc250743d4eb572d3617c4a4e08