configure: use canonical paths when comparing prefixes

A user reported in the mailing list [1] to be advised to use
`/usr/lib64/pkgconfig/../..` as a prefix. This path is too
convoluted, could give problems, and also shouldn't be the
one to be compared against the prefix flag used, so use
readlink -m to follow '..' subfolders to transform it, in
this example, to simply `/usr`

[1] http://lists.ximian.com/pipermail/gtk-sharp-list/2014-May/011436.html