Organizing and Analyzing Mounds of Research Text?

Andrew Green asks: "Four years ago, I stopped working on my Master's thesis in Social Anthropology. Now, I'm getting back to it again, and I find there's a _lot_ of text to deal with. I have a 350-page field diary, a dozen transcripts of recorded interviews, lists of books and articles, extensive notes about the books and articles, and the books and articles themselves in dead-tree or electronic format. I want to organize _all_ of it. I need to keep track of all the different text files on my computer (most are in MS formats, though I now use GNU/Linux), which ideally means keeping personalized sets of metadata about each file, linking files to other files and to entries in bibliography lists, and having some sort of version control. I'd also like to be able to do a free-text search on all texts on my local hard drive. And, most important of all, I need to build a hierarchical list of topics that are relevant to my thesis and relate specific sections of all these texts (not just whole files) to different topics. Any ideas? I know there are proprietary solutions out there, but I don't want to use them. What free applications can best deal with some or all of my needs? Would I be better off building something myself?"