Looking for a good document managing and annotation software

[TheSax]

Hello,
I am am looking for an app, that is able to

• manage documents (mainly by tags), without actually moving/rearranging the files in the finder
• "supervise" a folder (so that new docs automatically show up in the app)
• preview and annotate pdf, images and microsoft office files (while leaving the original files as they are)
• do all that stuff offline

Bonus points, if

• the app indexes the files instead of copying them somewhere
• the annotated file is (if possible automatically) saved next to the original one (pref. as pdf)
• it is possible to sync with an corresponding iphone-app (just to view the docs, there's no need to annotate something on the phone)
• (pdf-)documents can be tagged automatically according to the ToC

I am aware that there is probably no free app that can do all that, the only thing I don't want is a monthly fee.

Greetings
TheSax