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Eclipse is somewhat different to the rest of the IDEs because it allows to compile classes on the fly. But yet still Ext-Scripting and Eclipse are a good combination, but several things have to be taken into consideration.
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.
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.