Ubooquity is written in Java / Kotlin, and uses a Jetty embedded server and a H2 embedded database. Quite far from the PHP/MySQL stack.
So it won't be possible (and out of the scope of Ubooquity anyway).

However if the goal is to easily find what you are currently reading, a dedicated Ubooquity page with the "in-progress" is already on my to do list. It won't be part of the next release, but probably the one just after.

As for the favorites, I don't have plan to implement a "favorite" system, but there is already a column in Ubooquity for a user rating (unused so far, but it's a feature I'm considering).

This one's harder. Working on it...

I understand the usefulness of such a feature, but the design of Ubooquity makes its implementation quite complicated. I'll keep the idea in my backlog, but I don't think I'll tackle it soon.

You mean for a folder ? Or for a whole category (e.g. all comics) ?

I was not able to determine the cause of the issue (since I can't reproduce it on my side).

I will include additional debug logs in the next version, so that we can get more information about the reason some Djvu files can't be opened on your system.

The page title was not properly escaped, so the special character "&" in "Fantasy & SciFi" triggered the error.

This is fixed and will be in the next version.

Thanks for the detailed report, I will investigate !

Categories are just a way of organising your library.

There is no difference between categories regarding file format, or anything else.

That's part of why the development took so much time. On previous versions, books and comics were managed completely separately, with different code. Now every file is managed exactly the same way (with specific behaviour based on specific formats, e.g. the online reader, not categories). 

As for the "Calibre library" checkbox: when creating its internal folder structure, Calibre creates a folder for each book, which is annoying when you display the folder structure in Ubooquity.

Checking the box just hides the intermediate folder, removing an unnecessary click when you navigate.

You are using Java 8, the new version of Ubooquity requires at least Java 17, hence the crash.

Thanks for the feedback everyone ! :)