Bad news: version 2.0.0 does not include this feature.
(I forced myself to release as soon as the bookmark sync was done, for fear of starting another months-long development phase)

Good news: this special build does. :)

Add a file named themeScript.js at the root of your theme, it will be loaded by all Ubooquity pages (excepts the online readers and the admin page).
I started by adding a new "script" directory alongside the "theme" one, so that users could add it there. But I found it unnecessarily complicated when it could just be part of the theme.
As for security, I don't think people are going to read a script, even if you ask them explicitely to put it inside a specific directory. So it might as well be part of the theme.

Since the version is still beta, changes can still be made. Let me know your thoughts.

That's hard to say, especially since the PDF that triggered the error you showed me was correctly imported.

If you want, send me a full log (provided there are other errors inside, otherwise I won't find anything useful anyway). I'll take a look and try to understand what happened.

Given my rythm of release, I can't really advise waiting... ;)

(also, did you have the same problem with a previous version of Ubooquity ?)

Could you try with the following jar and let me know if it changed something ?

http://vaemendis.net/ubooquity/downloads/special/SimpletofMars/Ubooquity.jar

PDF is a never-ending source of pain. :D

The error you got comes from inside the PDF parsing library I use. Not much I can do about it unfortunately (without digging deep inside the lib, which I can't do).

I plan to allow using external PDF applications to parse the files (MuPDF, Poppler, seem to be quite good at handling all kinf of PDF files). It should get much better then.

As a side note, while I love the bookmarking, it would be wonderful to have a "recently read" or "currently reading" section of some sort so that I don't have to dig through my collection every time to resume a comic.

I almost started implementing this feature, then I decided to release this beta version instead. ;)

It's definitely planned !

The "UTF-8" parameter is sometimes needed to tell the Java VM (the Java process that runs Ubooquity) that the underlying file system is using UTF-8 encoding.

I don't know exactly why this is necessary on some systems, for instance I didn't need it on my Raspberry Pi (on Raspbian) and not on some others.

Did you explicitely authorize them for each folder you shared ? (the "people" icon next to the name of the folder in the folder list)

On Android you can use ComicViewer for Ubooquity or Challenger Comics Viewer.

On iOS there is Chunky Comic Reader.

I may have forgotten/overlooked some other apps...

Sorry, forgot to tell you: the admin page is available at http://myserver:2203/admin

If you run Ubooquity on a NAS, you'll access the admin page from another machine.

This is forbidden by default for security reasons.

You have to use the --remoteadmin option (I have update the release notes to emphasize this).

Let me know if this fixes your problem.