Here's a tool that I want. It's simple, and clearly useful. I study, as do many people, and I think the use case goes further. I have documents, which I don't need to edit -- e.g. articles and papers. I need to take notes against these documents. Further, I would like to be able to search within the body of documents and notes. I want to be able to create an articles hom directory (~articles). I then want to be able to have my own subdirectory structure (~articles/subject). I then want to be able to create notes files that are associated with each article. Then, I want a search tool (like Beagle or Google Desktop) which will constrain itself to ~articles, and know about the association between notes files and articles. I want full-text search, with a link on the results page to both the article and the notes. That would be great!