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One would most certainly exclude encrypted partitions from being indexed by Nepomuk for obvious reasons pertaining to private data protection.

Can it be imagined that Nepomuk/Strigi/Soprano... be able to manage more than one data store ? The usual one in ~/.kde/share/apps/nepomuk and others at /somewhere/encrypted/nepomuk for private data indexing. Whether all stores simultaneously or switching on/off some stores at will !

Or is it just technically too crazy to be conceivable ?

Thanks for considering.

You should encrypt your config/data dirs as well (e.g. .kde). It's likely there is more data about your encrypted files than you think.