Good points, but I think both methods could work together - first create collections based on directory structure and then add things defined in the playlist - this way you just manage the list of "duplicated" books instead of all books, so probably in most cases it would be just "favorites".
As for reordering, this can't be done using filesystem itself, but you can always check for a file named "order" or something (the reader doesn't display unknown extensions, so it wouldn't make any mess) if you really needed to place books in order different to alphabetical. In fact I find one disadvantage in using a list file - if you want the books sorted, you need to keep the list sorted
Similarly - you could check for some file that would tell the program not to create a separate collection based on this directory. And this would cover all the possibilities I think.
Anyway, these are just minor remarks -
great thanks for the program and the "filesystem collections" - I really hated creating them in Calibre (I'm a console creature - I prefer to type, than to click
)
As for linux build, I thought more about Borland Kylix - as far as I know it's free and it's been made to build Delphi projects on linux. But I could be not completely up to date.