Sounds like you just need a database. many about on the web.
As above Calibre specifically copys books to its own Library, and while I actually Hate that kind of behavior for music or videos, for txt files epubs mobi etc I think its great.
You could do it with Calibre though, I think.
Just have the entries be empty txt files. You could use a program like
http://www.sobolsoft.com/createfiletext/
looks like it may make empty txt files.
Good luck.
Not sure why you would want to though, as the reader in Calibre is great, and it opens txt and pdfs fine, plus ebooks are pretty small so even with thousands its still only a few GB, you could keep both your folder/directory structure and the Calibre library (backup if nothing else)