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For the Linuxcnc Raspberry Pi images just don't do dist-upgrade, it will break things, this has been proven.

You get get away without doing any kind of upgrade.

If you are worried about security, updates are only a small part of the picture. The first step should always be physical security, which should be the number one priority with a computer running a cnc machine.I'd take data loss over damage to a cnc machine any day of the week, you can't back up a cnc machine.

I would still appreciate knowing how to call anyone of these routines without going through the entire program.

You can call any subroutine in a loaded program from MDI (eg 'o100 call')

Also how to set the Z after the tool change.

Do you mean the tool-length offset or the work-offset?

The currently active work offset can be changed like this:
'G10 L20 P0 z123'