What about .3d files in different directories?

[tahina-pro]

#41 introduced module dependency analysis assuming that all .3d files are in the same directory. In #45, I heavily rely on this assumption when generating Makefiles by prefixing all source .3d files with the same EVERPARSE_INPUT_DIR variable.

However, as far as I understand, no guard has been implemented to explicitly forbid the user to call 3d --makefile (or 3d --batch on .3d files that do depend on one another) from several directories. Should we implement such a guard? If not, should we implement anything like F*'s --include ?

@aseemr @nikswamy What do you think?