Otherwise, we end up propagating those dependencies into targets that
link against that library, which creates unnecessary link-time
dependencies.
Also included are changes to readd now missing dependencies to tools
that actually need them.
We previously put the generated headers in SOURCES, which did not mark
them as GENERATED (and did not produce a proper dependency).
This commit moves all generated headers into GENERATED_SOURCES, and
removes useless header SOURCES.
