Compute flags for target in configure, not Makefile

[Alexandre Oliva]

This patch greatly simplifies the computation of most of the -B, -L
and -isystem flags that we used to do in the top-level Makefile.
Since all the needed information is already available for configure, I
propose that we move this computation to configure.

Another plus of this patch is that the long commands to compute these
variables used to overflow the maximum argument size of some systems,
when make tried to run the huge shell command to start sub-makes.
This will hopefully go away now.

Disclaimer: I haven't tested this on cygwin.  The patch reorders some
of the -I and -L flags, to keep the cygwin/winsup configuration
simpler.  If this should not be done, please let me know, and I'll fix
it.

Ok to install?