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I have the impression that if you want to clear history you have two (unrelated?) tasks.
You have to clear the caches and browsing history in .mozilla/eclipse and I do not see how the RSSowl interfaces permit that without resorting to manual rm. Then you have to
use the Tools->clean up menu and that cleans the sqlite databases in the --data directory (?). Is there a list of steps to thoroughly remove all the data both in the embedded browser and the data directory for a feed?
You are right about that.
'Tools->Clean Up' cleans up RSSOwl's internal feed database.
deleting .mozilla/eclipse cleans up everything from RSSOwl's internal browser (XULRunner).
Afaik there is nothing to remove both data.