... with make install.
It seems something like a SUBDIRS = io legacyio is missing in include/avr/Makefile.am. However, so far there is no autogenerated include/avr/io/Makefile.am to match the autogenerated io headers. I really don't know autoconf at all though, and my quick try with just SUBDIRS = legacyio did not lead to even just the legacy headers to be properly installed.