What i'm looking for could already exist, but i'm not sure how to find it.
a notetaker app that opens and structures a series of textfiles in a folder structure. At the moment most people either use software like onenote or evernote to keep all notes together, or plain text files scattered over their system. What I am looking for is to keep the flexibility of plain text (being able to edit/copy/rename/sync the node anywhere), but with some organising features - just some kind of tree structure where every node is an actual plain text file. Not the proprietary or database format used by all notetakers.
Quicknote comes close (
http://www.quicknote.de/qscreensen.php), but i just want to use my own textfiles in it, not use quicknote to create them then save them to text files.
I hope I make sense, please tell me if I don't

Sorry about the thread resurrection, but I was looking for the exact same thing.
I found a good one:
minipad2. It's really plain text, but you can reorder the nodes in the tree freely. (I wish more file managers could do this).
The default is to store notes in a db. but one can have virtual nodes that are real files. Also dragging and dropping a folder will create virtual nodes for all files inside it.