OK.

This e-mail is about file system checking in general, specifically
aimed at someone who needs to check /usr/local/games when it's part of
/usr

In order to check filesystems, you need to unmount them. [or risk
corruption (=]
There's a utility called "fsck". You've probably seen something about
it go past in the boot messages.

Anyway. What you need to do is drop to runlevel 1 [since /usr is a
partition, and nothing below it. If you'd made /usr/local/games
separate, you could unmount it, and check that while still in your
normal runlevel. But in runlevels 3,4,5 you'll find that lots of
daemons are running that have open files in /usr. so you won't be able
to unmount them]

To drop to runlevel 1, type in "init 1" as root. This _will_ destroy
anything you have running, so make sure to close all your work and
stuff.

You'll have nothing but either

1) a root prompt 
2) a login prompt
depending on how your machine is set up. If you get a login prompt,
log in as root.

Now, you need to umount /usr. If you get any errors about it being in
use, check that you're not in it in your shell. Also check the
results of "lsof". something like "lsof | grep usr" may show
things that're using stuff in /usr.

Kill anything that's using files in it.

Now, check it. "/sbin/e2fsck -v -f /dev/hde11". Or whatever partition
/usr is. RTFM. You know the routine by now.

Anyway.

Theoretically, you can now go back to runlevel3 [or whatever your
default is] and it should mount filesystems that should be but aren't,
etc, etc. Whether or not it will is relevant to your distribution and
personal taste. I've reconfigured so much of my machine I can't even
remember whether or not it does it by default here...

Other things?
If you've done something truly stupid, as we have all done at some
point or another, all is not always lost.
If, for example [painful example], you've run "mkswap" on a partition
that you didn't mean to, you don't need to re-install it [usually].
e2fs keeps one [sometimes more] extra copies of your superblock. Look
at the man page for e2fsck to find out how.

In fact, just by the way, I must make a humble recommendation: read the
manpages for both fsck and e2fsck before even attempting any of the
above
Of course, in the end, you'll probably actually want to print these
out, because if something goes wrong, you're gonna need them, and it's
not gonna go wrong in such a way as you'll be able to read the man
pages afterwards (=

Anyway.
Hope this all helps,

Gary (-;

PS If you want to know more about runlevels and how to start services
[ie, what the hell is going on with all those /etc/rc?.d directories],
have a shufty at other things in this dir.