Fix the directory target generation

The directories for the final products were never registered, it was
plain luck that intermediary files were in the same place and
registered the directory anyway.

Also, scripts are generated directly from source (binaries go through
intermadiary object files), so we need to explicitely make sure to
avoid registering the source directory unless it's an in source
build.

Reviewed-by: Andy Polyakov <appro@openssl.org>
Reviewed-by: Rich Salz <rsalz@openssl.org>