[smoker]

FBreader was actually my first thought as you can define a folder and then it automatically scans the folder and imports the books (in contrast to most reader that you have to press the button first). But I find the lack of modern shelve-like UI annoying... Mantano looks good to me, but I find the lack of preassigned categories annoying and also whats the purpose of the mantano cloud??? you can't even upload books from your computer!!!

Edit:

I found a solution, still not exactly what I had in mind but it will do. I had decided that the only way was to use tags in order to short the books the way I wanted but while I was playing with Mantano reader I found out that besides tags they also can show up the folders the books are in! So I can sync with dropbox and then set only these two folders in Mantano reader to import books from. and I say it is not exactly what I had in mind because it shows the full path and I cannot set it as the direct view when the reader starts... Still, it is good enough!