Sorry, I have missed your reply :)
You can check by running 'echo $SHELL' while inside the shell. You can change default shell in Ajenti by going to Configuration > Plugins > Terminal.

Progress of long-running operations can now be seen in Tasks section

This means that Ajenti port (8000) is used by other application. Check with 

sudo netstat -tlnp | grep 8000

Ajenti doesn't include any third party software.

Sorry for the delay. This is not possible at the moment; classconfigs are bound with simple bind:dict, which only allows binding one level of scalar values.

If you need a complex configuration tree, I suggest instead saving it to JSON or use a more convenient config-to-object binding Reconfigure (https://github.com/Eugeny/reconfigure)

Can you verify the credentials with 'mysql -u.... -p....' ?

You can setup OS user sync (Configure > Users > Sync) and use actual password of the user to log into Ajenti :)