[Sluglug] Partition Question

[Erich]

Greetings! I, too, am a Freshman here at UCSC - Bioinformatics major. I've
been running Gentoo (amd64~) for almost a year now, but have started to
acrue quite a few "Error: disk hda3 uncleanly mounted. Non-contigous files:
3.5%" errors. That's nowhere near a direct quote, but I think you get the
idea.

So that's got me wondering - though I use all ext3 (journaling enabled)
partition schemes (except for /boot {hda1}, which is ext2), I'm getting
fragmentation issues. I looked around for a defrag utility, but the only
thing I could find was a some mail list that said that if you had enough
space on your disk, you could: (as root)

mkdir /bak
cp -r /* /bak/   (not sure if -r is needed)
mv -r /bak/* /   (same)

That seemed so incredibly dangerous that I didn't even think about doing it.
Also, I should note that that error doesn't always show up (the
non-contiguous error). So here're my questions: 1) What exactly is going on
here? 2) Do I need to fix it? 3) How?

Thanks!

~Erich Blume