Your comments

Ubooquity already supports ComicRack XML metadata files (since 1.7.0).

What features would get from a direct database integration ?
Given the insane pixel density we have today on monitors, I get how this would be nice.

It will require a heavy modification of the reader script though. I'll put it in my todo list (I think it's a good idea), but don"t expect it anytime soon.
I'll focus on the read/unread flag for now. ;)

Sorry, I'm quite late. Here is the line modified with the encoding option (and the new "workdir" parameter):

exec /var/packages/JavaManager/target/Java/bin/java -Dfile.encoding=UTF-8 -jar -Xmx1024m /var/packages/Ubooquity/Ubooquity.jar -port 2202 -webadmin -workdir "/volume1/prive/Ubooquity"

Thanks for the feedback and help !

As for the "user.dir" replacement by the "workdir" option, it's on me.
I told Matthew I would change it. It'll be done soon.
Unless there is a bug I don"t know about, the cache folders (books and comics) are cleared when you click the "clear database" button. There is no need to clear them manually.
And this will indeed rebuild your whole database, rescaning all files and regenerating all covers.
It has to be in the command line you use to launch Ubooquity.

So if you followed Matthew's tutorial, you have to modify the /etc/init/ubooquity.conf file.
If you want, just post here the script you use to start Ubooquity and I'll indicate what changes to make.