Question #688284 on Sikuli changed:
https://answers.launchpad.net/sikuli/+question/688284

RaiMan proposed the following answer:
I checked with version 2.0.2:

- I have a jython installation at c:\jython2.7.1
- the folder contains a jython.jar

Find and open or create the file extensions.txt in the SikuliX-Appdata
folder in Extensions.

Add a line to the file as:
jython =  c:\jython2.7.1\jython.jar

In the extensions folder put an existing jython...jar to a subfolder
like _hidden (just to still have it, but out of reach for SikuliX).

now start the IDE from commandline using

java -jar sikulix.... -v -c

to get the startup dump.

You should see, that the extension.txt content is recognized and that
(at the end of the dump) your jython is on the sys.path.

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