GPS includes basic facilities for refactoring your code. Refactoring is the standard term used to describe manipulation of the source code that do not affect the behavior of the application, but help reorganize the source code to make it more readable, more extendable, ...
Refactoring technics are generally things that programmers are used to do by hand, but which are faster and more secure to do automatically through a tool.
One of the basic recommendations when you refactor your code is to recompile and test your application very regularly, to make sure that each of the small modifications you made to it didn't break the behavior of your application. This is particularly true with GPS, since it relies on the cross-references information that is generated by the compiler. If some of the source files have not been recompiled recently, GPS will print warning messages indicating that the renaming operation might be dangerous and/or only partial.
One of the reference books that was used in the choice of refactoring methods to implement is "Refactoring", by Martin Fowler (Addison Wesley).