Fix dependency scanning configuration in subdirectories

Refactoring in commit v3.5.0-rc1~347^2~2 (Set the current dirs on the
snapshot before creating the cmMakefile) accidentally changed the
source and binary directories configured in `cmake -E cmake_depends`
for use during dependency scanning.  This can cause the wrong directory
information to be loaded.  It also breaks Fortran module dependency
scanning for modules provided by targets in subdirectories that do
not have Fortran_MODULE_DIRECTORY set.

Fix the dependency scanning directory configuration and add a test to
cover the Fortran module case in which the breakage was observed.

Reported-by: Kelly Thompson <kgt@lanl.gov>