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Intellij is very specific because it allows mixed programming out of the box, hence it is the ideal partner for mixing it with Ext-Scripting. However while setting everything up you have to be aware of several specifics.
If you only have one sourcepath you might have a look at the package whitelisting to mark only the packages you actively want to edit for this deployment cycle. This speeds up startup time and helps generally to avoid restarts.
If you use different paths then you can work by including the added source paths as sources like WEB-INF/java or WEB-INF/groovy (not classes compiled via Ext-Scripting always have higher loading priority than what can be found in WEB-INF/classes), so there is no need to change any target directories source directories always are enough.
To change your source directories open File->Project Structure->Modules-><Your Web Module> and mark your script directories as source paths:
You can leave your compile target directory unchanged
If you prefer your own source paths to be the sources of everything set the org.apache.myfaces.extensions.scripting.java.LOADER_PATHS or org.apache.myfaces.extensions.scripting.groovy.LOADER_PATHS accordingly in your web.xml the same goes for the resource roots.