Add warning message that non-EDM files will not be published

The warning message is printed only if the CMSSW pset produces TFiles or if the user specified additional output files to be collected.
I also moved a check that we had about the publication and transferOutput flags not being respectively True and False, inside the validateConfig() function of submit (it was inside the __init__() of SubCommand).
I also moved a check that we had about the storage site being specified if transferOutput or saveLogs flags are True, inside the validateConfig() function of submit (it was inside the __call__() of submit).
The rest of the changes in the commit are just to make the code more readable (IMO). Sorry for making such changes. Tell me if you don't want me to do this.
This pull request is for issue https://github.com/dmwm/CRABServer/issues/4358