[isabelle] Isabelle/Jedit not recognising theories in menu



Hi,

After I start up Isabelle and load some theories
I can no longer switch between theories by clicking
on the theory name in the theory menu.

I'm using Isabelle2016-1 on a Mac (Sierra).
I've tried reinstalling Isabelle2016-1 and
removing .isabelle/Isabelle2016-1 from my home.

The problem also seems to have ported itself
to Isabelle2016 somehow?

Are there some separate magic files for jedit that have
become corrupted?

Thanks in advance
Ian





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