Hi,
  * make 'fhs' the default filesystem layout (so, by default everything is 
installed in /usr/local/
    using a Unix layout) (with the exception of apple-apple-apple because there 
people are using
    gnustep-make to compile Apple stuff, they're not really installing GNUstep)
Fine.
I still dislike this default. Am I really the only one?
  * add help for how to use each filesystem layout (printed at the end of 
configure)
Fine.

Very fine. Also make sure, for the layouts that need "GNUstep.sh" to be sourced, that if possible a decent message is printed out. We might need to update gnustep-make and the makefiles generated by, for example, ProjectCenter and check the makefiles of stuff generated manually. A standard message will help the user who choose that kind of installation.

  * (potentially, this is a new idea) rename 'fhs' to 'unix' ?
Not sure if this is a good idea.
I don't think either. It is the FHS buzzword that people expect when they are choosy and want FHS. Unix appears to be to generic.

Just my 0.2 €

Riccardo

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