Answer to Q1)

Yes, assuming you are using the admin user login, use sudo before the command you want to run as root, you will be asked for the admin users password. See FAQ: How to access a JumpBox as root.

Answer to Q2)

Xwindows and other GUI components are not installed on any JumpBox by default for space reasons.

Answer to Q3)

Good point, I guess we may not have adequately documented that in the README.txt. A self signed SSL certificate is generated the first time you boot the JumpBox. If you choose the "it just works" setting, it will use this certificate and make the application available on the SSL port (443) in addition to the HTTP port (80). We do not force traffic onto one or the other (though may in the future or add an additional option) so it is up to the users to use http or https (or someone to make a manual web server change, this has been done somewhere in the forums). This self signed cert is an OK, though not perfect SSL solution for internal type usage but definitely NOT appropriate for financial type or other sensitive transactions.

Now for your problems ....

P1)

The files are in /var/data/mediawiki and I think writable by the admin user, if not you would use sudo to start the nano text editor on a file like this:

sudo nano /var/data/mediawiki/LocalSettings.php

P2) I do not understand. Are you saying you are typing it in the URL bar? Have you reviewed the Mediawiki Documentation for what you are trying to do?

P3) Also not sure what you mean, by default the pages are editable for even unauthenticated users (unless a recent version has changed) if not then they are certainly editable if you log into mediawiki as the admin user (using the same password set at setup and used to SSH in).

P4) If you are using a registered JumpBox (which if you have shell access you presumably are), you can disable the JumpBox navigation bar at the top by following the Disable Navigation Bar instructions.

Good luck and I hope this helps,
Austin