Upgrade base system to Ubuntu 24.04

[gouttegd]

This PR updates the base system of all our images to the latest LTR version of Ubuntu, 24.04.

• Some system packages that were previously implicitly installed now need to be explicitly asked for (e.g. libpcre3, needed for Konclude, or npm, needed to install Obographviz).
• The OBO Dashboard must now be installed with --break-system-packages, otherwise pip will by default refuse to install it system-wide (the idea is that only APT tools are allowed to install anything system-wide).
• We can no longer have virtualenv in the builder image, as it messes with the installation of our Python packages.
• The odk.py script has some issues with Python 3.12 that need fixing.

closes #1008

[gouttegd]

(For those keeping track, this the same PR as #1067 modulo the wording of some commit messages and freshly updated Python constraints.)