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The ext3 /home partition on my laptop is a little bit fragmented. I think it's because I access it from within Windows as Thunderbird shares the Linux profile. Same thing a few other things I'm working on (documents, source code etc.)
For defragmenting the ntfs partition I noticed that O&O Defrag seems to do it a little different from the standard Windows tool. After a defrag Windows boots a little faster and idem for startup speed of programs like Eclipse & Firefox.
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