Make provisioning scripts run in unprivileged mode + more

[MakisH]

The main goal of this PR is to solve #16 and simplify unreasonably complicated commands such as

- sudo -u ${USER} mkdir -p /home/${USER}/Desktop
- chown ${USER}:${USER} /home/${USER}/Desktop
---
+ mkdir -p ~/Desktop

or

- sudo -u ${USER} git clone --depth=1 --branch master https://github.com/precice/calculix-adapter.git
---
+ git clone --depth=1 --branch master https://github.com/precice/calculix-adapter.git

Apparently, Vagrant runs as root by default, which complicated everything, but it also provides a privileged: false mode:

- config.vm.provision "shell", path: "provisioning/install-basics.sh"
---
+ config.vm.provision "shell", path: "provisioning/install-basics.sh", privileged: false

The scripts now make much much more sense and are pretty much ready to use with any other environment (Docker, GitHub Actions, or even as installation examples).

I changed the hashbang to #!/usr/bin/env bash, as the Vagrant documentation was using that, I am using a bash feature (grouping echo commands), and it is still quite portable.

At the end of the Vagrantfile, the provisioner deletes all compiled object files in home, to save space (script cleanup.sh). We were already doing this for SU2 before. This step is commented-out by default, to facilitate development. It is mainly relevant for the packaged box.

All scripts are formatted and checked with shellcheck.

Summary:

• Closes Permission errors in repositories #16 (main point).
• It looks like is also closes FEniCS is not working #4, even though I am not sure if this PR fixes it, or if it was fixed upstream. The additional step to uninstall fenics-ufl is not needed anymore.
• It also closes Need to move tutorials and examples to the home directory, link from Desktop #8 (moving tutorials to home) and closes Missing deal.II solvers in PATH #9 (updates for the latest deal.II adapter). Sorry for the mix, I really wanted to push the VM forward.
• Partial solution for Firefox bookmarks and homepage #13 (adding one link to the VM page on the Desktop).

After merging, update the website:

• deal.II adapter: remove additional steps
• move install-vscode.sh
• add a note about vagrant ssh and vagrant ssh -- -Y (not related, but we don't advertise this)