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Although a little unfortunate, I see no better solution than establishing the "convention" of replacing dashes with underscores in package names in order to have unique paths to Groovy scripts. This convention is also endorsed somehow by Oracle itself https://docs.oracle.com/javase/tutorial/java/package/namingpkgs.html 
PM too seemed    PM too Christopher Zimmermann seemed to be able ("can able "™) to live with it (maybe he even suggested it, can't recall) 

Next steps and more questions

If the solution outlined here and in the PoC is validated here's what would be left to do

• adapt Groovy module tests to use Resources API
• migrate enabled Groovy sources (non script ones) from the scripts to the resources workspace. Groovy source is found in a property called text which is also available for resources.  
• remove the script and enabled fields at /modules/groovy/apps/groovy/subApps/detail/editor/form/tabs/script/fields and their values in the remaining scripts in the scripts workspace.
• move/adapt Groovy validation to Groovy files in resources, e.g. when created in the app or hot fixed
• still re validation, how to signal an invalid (syntax, package matching folder structure under module) Groovy file when working on the file system? 
  • in dev mode observe Groovy files via Resources API and validate on resource added/changed?
• Do all these novelties and changes require a new major version, i.e. 2.5 ? Probably they do.
  
  
  
  /modules/groovy/apps/groovy/subApps