Resolves absolute against your Eclipse workspace:
include("workspace://ScriptProject/helloWorld.js")
... includes the file helloWorld.js from the workspace project named ScriptProject.
Resolves relative against the current project. Relative links always need a reference to compare against. By default the currently running script location will be used as reference.
include("project://ScriptProject/helloWorld.js")
... expects that helloWorld.js exists in the same project as the script that calls include().
Resolves absolute against the repository of registered scripts. The path to be used is the same as displayed in the Script Explorer view.