Just realized I replied to this off-list and wanted to post my response 
publicly for posterity (sorry to spam, Chris)

This is an excellent question and it's very exciting to hear that a NetLogo 
package is in the works for Gentoo! In general, I see two approaches you 
could use when it comes to configuring NetLogo:

   - Write the installer in such a way that the NetLogo.cfg file is 
   generated based on the system setup at the time of the install. This avoids 
   hardcoding a value into NetLogo.cfg, but the value ends up being an 
   absolute path on the user's computer. I don't know anything about building 
   Gentoo installers, so I'm not 100% sure this is possible / feasible.
   - Include a launcher script instead of the launcher executables. The 
   bundled netlogo-headless.sh is a good place to start. You will need to 
   change org.nlogo.headless.Main to org.nlogo.app.App (and add in system 
   properties / java arguments from the NetLogo.cfg file) but this allows you 
   to base the launch off of the user's JAVA_HOME. Another benefit of using 
   this method is that the .so files in the project root don't need to be 
   included with the NetLogo installation (the various graphics .so files will 
   need to be included).
   

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