all_flags.pb: Properly handle intermediate files am: 194d492d am: c415968b

Original change: https://android-review.googlesource.com/c/platform/build/soong/+/3106680



Change-Id: I0923074cb2d6e99c2fa25a52dd1d2b7c58c7562b
Signed-off-by: Automerger Merge Worker <android-build-automerger-merge-worker@system.gserviceaccount.com>