Fix incrementality bug with merged BUILD files

The merged build files should be added as ninja dependencies,
so we rerun when they're changed.

Fixes: 246552590
Test: m bp2build, m bp2build again and observe it didn't rerun. Then add a comment in external/protobuf/BUILD.bazel, run m bp2build again, and observe it reruns
Change-Id: I26ed035cc0a894500a192f9aa3371fb46519689b