hdf5doc

Purpose:
Bug fix

Description:
Parallel builds were breaking in tools/lib

Solution:
talign didn't realize it depended on libh5tools.la because its
dependencies listed the full path (../../tools/lib/libh5tools.la).
Changed this, and made similar changes in a couple of other
directories.
This checkin should also add the --foreign flag to every Makefile.in

Platforms tested:
sleipnir (minor change)