We also use one shortcut per project and each project gets its own config#.fpw where # == major version number of VFP. The config#.fpw sets path, default and IDE caption, and it also sets resource to FoxUser#. If there are plain config.fpw/FoxUser.dbf then they are for the app, so the app won't accidentally pick up the dev env settings when tested.
This way each project 'remembers' its environment, including _command, prefs, recently used files, open PJXes etc. pp. and you can jump right in where you left off, even weeks later.

> I am using VFPSP4 and have been encountering problems where VFP mixes up
> method code of two classes with same name and same method name from two
> different projects. (Bug?)

Could you be a bit more precise, please? Are you saying that the filename in sys(16) differs from this.ClassLib when you execute a method defined by the class? Or are you just unsure where your object instances actually hail from because set("PATH")/set("PROC")/set("CLAS") have gotten out of hand?