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Organize bookmarks in non-browser format?

I'm trying to organize my bookmarks and I think I'm kinda screwed now.

For a few years now, I've been keeping my "most important" links in plain HTML files which I set as my Homepage with tabs at the top for Main, Software, University, Research, etc. instead of using my browser's bookmark organizer. It works(ed) quite well. But, over the years, and a few thousand bookmarks now, its completely unmanagable to sort through. I have a good idea of what I want to keep. Worse, I've been saving bookmarks in different browsers so I have some in Safari and Firefox.

I used cp to join various bookmark files I backed up (and there were many duplicates in the files). I then used unix tools like grep, sed and sort to delete duplicate bookmarks and bookmarks I don't need. I don't know a lot of scripting so I'm at the limits of my abilites. I'm sure there's a nice way to do it in a programming language.

Since my bookmarks are now plain old HTML links, I'm finding it really hard to use a program to import my bookmarks. Most browsers will choke on the amount of bookmarks (and I don't intend to keep them all). I've look on Freshmeat and Sourceforge for a solution but most software or scripts avilable require the bookmarks to be in Firefox-ish style which means I have to add all the markings I stripped out - I've tried said software/scripts and it won't work. Most software available only neatly imports bookmarks when they are in Netscpae/Firefox format.

So what should I do?

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