There are some programs that have such complicated initialization files that they don't recommend, or even want, for you to edit the file yourself. One example of this is Pine, the mail program. All changes to it can be done through the setup-config options in Pine. You can still edit this file by hand, but be wary of mistakes. If you get it too fouled up, you'll have to delete it and redo the configuration using Pine again.
Most complex programs have the ability to read initialization files.
This includes all the editors we have, the compilers, and some of the specialized text formatting programs. Start by using the program for a while, and then think about the options that you find most useful. These are the ones that need to be initialized somehow. The information included here is for the University of Alabama central computing facility as it was configured on the document date. It may or may not apply to other Unix systems.