Protege 4.2 configuration files on Linux / Ubuntu 12.10

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Protege 4.2 configuration files on Linux / Ubuntu 12.10

Davide Sottara
I have installed Protege 4.2 on a Ubuntu 12.10 64bit machine.
I have noticed that some Protege configuration files - ontology
preference, tab config, view layout, xml writer -
are persisted in an odd-looking position under ~/.java/.userPrefs.
This is the "root" folder on my machine:

The main issue is that the configuration files there persist between
installations. I have recently upgraded from
Protege 4.1 and Protege 4.2beta to Protege4.2 final. At some point,
these settings got corrupted and Protege 4.2
started to behave erratically - the view would not refresh correctly and
reflect the state of the internal model,
so that edits would be applied to the wrong classes/properties.
Interestingly, reinstalling Protege did not have any effect, but
resetting the UI to its default state solved the problem -
which led me to the files above.

If this is not a bug but an intended feature to preserve user settings,
shouldn't the documentation include
a reference to the various configuration file folders? And btw, is the
folder name above normal?

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