For ld -r, we generally set the VMA of sections to zero. This is done
to make the output of ld -r most similar to that output by the
assembler, which generally has sections starting at VMA zero. In some
cases that covers for backend bugs which would mis-handle relocatable
object files with non-zero section VMAs.
This patch fixes a few sections that didn't have zero VMAs for ld -r.
A missing zero on .note.gnu.build-id and .eh_frame_hdr doesn't matter
much since these are linker generated symbols only output on final
link, but it's good to be consistent.