When using the per-target runtime build, it may be desirable to have
different __config_site headers for each target where all targets cannot
share a single configuration.
The layout used for libc++ headers after this change is:
include/ c++/ v1/ <libc++ headers except for __config_site> <target1>/ c++/ v1/ __config_site <target2>/ c++/ v1/ __config_site <other targets>
This is the most optimal layout since it avoids duplication, the only
headers that's per-target is __config_site, all other headers are
shared across targets. This also means that we no need two
-isystem flags: one for the target-agnostic headers and one for
the target specific headers.