The title is kind of confusing. If you have already installed knoppix on flash, and you
have enabled a persistent store, meaning you could go ahead with adding, upgrading
and customizing packages, why do you still need to re-master knoppix ?

Reasons as follows :-

1. When you upgrade your files/packages, the original copy resided on the
read-only compressed image is still there. The system exposes you to the ones on
the persistent store, and hides away the ones on the compressed image.

This is a waste of space, if you have upgraded many files/packages, for
every file/package in the persistant store, there is a counterpart in the
compressed image. Re-master will delete the hidden copies.

Even when there is no compressed image counterpart, due to you added some
new interesting packages, by moving your added packages to the compressed
image, you also free up the (uncompressed) space on the persistent store.

2. Another reason to re-master is that you want to maintain a clean separation between
experimental things verses the "stable" portion of your customization, ie you want to
move the stable and proven things to the compressed image, so that you can later
proceed to add your experimental things to the persistent store. In case you
are not happy with the new experimental things you added, you can always erase it
from your persistent store, or even you can wipe out the entire persistence store.
If you have previously re-mastered your flash installation, deleting things from the
persistent store is an easy, clear-cut and safe operation; because even if you delete
everything, you will still have the last snapshot of a fully working, stable and proven,
and yet already fully customized version of knoppix to start with. There is no need
to falling back to original uncustomized knoppix.

The end result of a flash re-master is not a new copy of CD or DVD, as you have already
booted off from flash, CD or DVD is irrelevant. The end result of flash re-master is just a
new copy of compressed image KNOPPIX.

This is how I re-master my flash installation, in brief. Note there is no "chroot" needed :-

Find a directory or a partition where you have a few GB of space :-
# mkdir -p /lots_of_free_space/source/KNOPPIX
# mkdir -p /lots_of_free_space/master/KNOPPIX
# cd /lots_of_free_space/source/KNOPPIX
# cp -a /dev .
# cp -a /UNIONFS/bin .
# cp -a /UNIONFS/etc .
# cp -a /UNIONFS/lib .
# cp -a /UNIONFS/sbin .
# cp -a /UNIONFS/usr .
# cp -a /UNIONFS/var .
# cp -a /UNIONFS/opt .
# cp -a /UNIONFS/home .
# cp -a /UNIONFS/root .
( Whatever you want it to appear in the new compressed image, you copy it there )

# cd ..
# mkisofs -R -U -V " filesystem" -publisher "KNOPPIX" \
-hide-rr-moved -cache-inodes -pad /lots_of_free_space/source/KNOPPIX \
| nice -5 /usr/bin/create_compressed_fs - 262144 > /lots_of_free_space/master/KNOPPIX/KNOPPIX

After a long time, you will get a compressed image at /lots_of_free_space/master/KNOPPIX/KNOPPIX,
which you can use it to replace your /mnt-system/KNOPPIX/KNOPPIX.

You can see that the steps above are quite simple. This last step of replacing existing KNOPPIX
compressed image must be perform "offline", ie you should perform it when you are not
using /mnt-system/KNOPPIX/KNOPPIX.

There is a challenge, because once you have booted in knoppix, you are already using
/mnt-system/KNOPPIX/KNOPPIX. So either you boot from a CD with your flash detached
and then put the flash back after you have booted so that you can overwrite it, OR you
could configure /mnt-system/boot/syslinux/syslinux.cfg to add the cheatcode "debug"
in it. At the first shell prompt, the /mnt-system/KNOPPIX/KNOPPIX is not mounted yet,
this is when you could manually perform this somewhat "risky" task.

Basically the steps will be roughly like this :-

If your free space which contains the compressed image resides on a separate partition :-
# mount /dev/sdaX /lot_of_free_space
If you have enough space, you can rename KNOPPIX for backup purposes :-
# mv /mnt-system/KNOPPIX/KNOPPIX /mnt-system/KNOPPIX/KNOPPIX.bak
Now overwrite it with the re-mastered copy :-
# cp /lots_of_free_space/master/KNOPPIX/KNOPPIX /mnt-system/KNOPPIX
You can skip mounting knoppix-data.img by renaming it,
# mv /mnt-system/KNOPPIX/knoppix-data.img /mnt-system/KNOPPI/knoppix-data.img.bak
If using the cheatcode "debug", once done, you type "exit" to proceed with the rest of booting
to verify that you new image is working. You will have to exit 6 times before it will be booted

If you are happy with it, you can shutdown and boot another time into "debug" shell, this time
you can "restore" your knoppix-data.img and free up the space in there :-

# mv /mnt-system/KNOPPIX/knoppix-data.img.bak /mnt-syste/KNOPPIXknoppix-data.img
# mkdir /tmp/tmp
# mount -o loop /mnt-systsem/KNOPPIX/knoppix-data.img /tmp/tmp
( Now you can delete whichever files you want to delete to free up the space, as
they have already been transferred to the compressed image ).
# cd /tmp/tmp
# rm -rf bin sbin lib etc var usr .......

Once you have finished :-
# cd /
# umount -d /tmp/tmp
Again, if you are using "debug" cheatcode, you have to type 'exit' 6 times before you
will be booted completely with the freed-up persistant store.

In any case, the steps above involved will be somewhat tricky to the Linux newbies. I wish there
is a cheatcode called "upgrade=/dev/sda4:/master/KNOPPIX/KNOPPIX" which will automatically
perform the upgrade. I will leave this as an exercise for those interested to do so by modifying minirt.gz.

Last note: the "debug" cheatcode is a very useful thing. As you can use it to rename/move the
knoppix-data.img ( or knoppix-data.aes ) for the purpose of resizing.