Linux – Any way to limit disk usage on a per directory level

I would use rsync as it means that if it is interrupted for any reason, then you can restart it easily with very little cost. And being rsync, it can even restart part way through a large file. As others mention, it can exclude files easily. The simplest way to preserve most things is to use the -a flag – ‘archive.’ So:

rsync -a source dest

Although UID/GID and symlinks are preserved by -a (see -lpgo), your question implies you might want a full copy of the filesystem information; and -a doesn't include hard-links, extended attributes, or ACLs (on Linux) or the above nor resource forks (on OS X.) Thus, for a robust copy of a filesystem, you'll need to include those flags:

rsync -aHAX source dest # Linux
rsync -aHE source dest  # OS X

The default cp will start again, though the -u flag will "copy only when the SOURCE file is newer than the destination file or when the destination file is missing". And the -a (archive) flag will be recursive, not recopy files if you have to restart and preserve permissions. So:

cp -au source dest

If you're forced to use ext3, then using LVM is probably your best solution. Create a new filesystem per project. That would look something like this:

# Create a 10g filesystem for "project1" in volume group "vg0"
lvcreate -L 10g -n project1 vg0

# Create an ext3 filesystem.
mke2fs -j /dev/vg0/project1

# Mount it (obviously you would want this in /etc/fstab)
mount /dev/vg0/project1 /projects/project1

Growing the project filesystems is easy:

# Add 2GB to the volume.
lvextend -L +2g /dev/vg0/project1

# Grow the filesystem.
resize2fs /dev/vg0/project1