"At least one general function requires a format validation which is contained in the Spec.pm library"

Sounds like this is the dependancy you need to remove. The program/general-library should not know the validation piece exists.

Meanwhile, what you really need to do is modularilize your program so that you don't have to export anyting. (Perl OOP -- when done at a minimal level -- isn't that painful and it doesn't have to be overdone if you don't want to overdo it).