Reorder Makefile variable setting and change some names.
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Description

Reorder Makefile variable setting and change some names.

* src/gpg4win.mk.in: Move setting of bdir, idir, et all to  ...
* src/Makefile.am: here, where we already set the root dir var.
(native_idir): Rename to nat_idir.  Change all users.
(native_ipdir): Rename to nat_ipdir.  Change all users.
* src/gpg4win.mk.in (pkgpbdir): Rename to pkgpatbdir.
(pkgpdir): Rename to pkgpatdir.

This should make things easier to understand. Also documented the
directory names.