Thanks for all your replies.
Originally Posted by dassie
You could upload all your epubs in your preferred folder structure to a website (or run one locally) that allows for directory listings. Then use the browser on the Kobo to navigate your folders and download the book to read/add to the kobo's library.
I though about porting (more like compiling) httpd to kobo and use the internal browser for everything. But then I need to disable the library indexing function for these files.
I read that you can trigger the reindexing by manipulating a file and making nickel think that usb was pluged in an out.