run-script: fix argument checking

The first argument is not the name of the script file,
but rather the identifier of the module to process.
ScriptGenerator: generate Python stubs, not Jython

We no longer need to use Jython specifically, since we are just spawning
a new JVM anyway.

More importantly: calling Jython from OMERO does not work as is, because
the classpath includes an incompatible version of ASM (needed by OMERO)
that results in Jython throwing an exception during initialization.
README.md: remove Jython from the instructions

The ImageJ script wrappers now use Python instead, which is already a
prerequisite of OMERO, so no more need for the extra Jython dependency.

Besides, calling Jython from OMERO did not work due to a version
conflict between Jython and OMERO regarding the ASM library.