[PATCH] Always call mkdir-init, even if we're not in a VPATH setup (Fixes Issue #2032)

* configure.in: Always call mkdir-init, even if we are not in a VPATH
setup. This fixes issue 2032.
* build.conf: Removed mkdir-init from all dependency lists because
it's now always run inside configure. This change also prevents make
from unnecessarily recompiling targets just because the file
'mkdir-init' does not exist.

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