Question #196620 on Sikuli changed:
https://answers.launchpad.net/sikuli/+question/196620

RaiMan proposed the following answer:
The original sikuli-script.jar is a hybrid in the sense, that it contains Java 
code, Python code, native code and the Jython interpreter.
With your approach, you only get the Java stuff. The rest is scattered around 
(sorry to say, but sikuli-script.jar is a mess ;-) in the sources, the libs and 
the build folders.

So to build the jar, as it comes with the package, you have to go a
rather painful way, that cannot be setup with the standard project
features of Eclipse.

This is the reason, why I decided to make an ANT build.xml (which is the most 
Eclipse like make option).
This is listed in comment #1.

One more thing: I recommended NOT to copy all the needed stuff INTO your 
Eclipse project. Even the source and the target folders (containing the 
compiled class files) can be implemented as references to the outside world.
What is available outside should stay there and be referenced in your project 
only.

--- the big jar
since you copied everything into the project, everything goes into the jar. 
Since it is not possible, to build the jar as it is needed from within your 
Java project without modifying the build files, I find it easier to make a 
separate build workflow, that puts the pieces together including the correct 
manifest.

--- recommendation
Try to understand the steps I have setup in the build file in comment #1 (it 
should be rather easy to read) and then decide, how you want to make your 
sikuli-script.jar.
As already stated: I have decided to keep as much as possible outside of the 
Eclipse project folders, so I let the class files be stored in my build folder 
in my local github fork. To achieve this, I have defined some path variables.

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