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

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



Change-Id: I84c197a93b852bfe7a00566d15d5e7b02fa19328
Signed-off-by: Automerger Merge Worker <android-build-automerger-merge-worker@system.gserviceaccount.com>