The Autoconf manual says:

     Posix 1003.1-2001 requires that `cd' and `pwd' must update the
     `PWD' environment variable to point to the logical name of the
     current directory, but traditional shells do not support this.
     This can cause confusion if one shell instance maintains `PWD' but
     a subsidiary and different shell does not know about `PWD' and
     executes `cd'; in this case `PWD' points to the wrong directory.
     Use ``pwd`' rather than `$PWD'.

so this commit replaces all uses of $PWD by `pwd`.

Reported-by: Justin Pettit <jpettit@nicira.com>
Signed-off-by: Ben Pfaff <blp@nicira.com>