Redmine

Configuring Redmine is pretty easy since most of the configuration is stored in database.
Using Ruby for writing such CLI would be trivial since Redmine is written in Ruby itself.
To create such tool basic programming knowladge would be necessary.

As a starting point you can use code snippet below in order to load Redmine enviroment:

#!/usr/bin/env ruby

require "#{REDMINE_ROOT}/config/boot" 

# now you will have access to full Rails and Redmine API
Setting.ui_theme = 'yourtheme'

Here are several simple examples of Redmine settings:

cat << "EOF" | bundle exec rails console production
Setting.ui_theme="alternate" 
Setting.welcome_text="My welcome text" 
Setting.host_name="redmine.foo.bar" 
Setting.app_title="My Redmine" 
Setting.mail_from="redmine@foo.bar" 
Setting.emails_footer="My footer" 
quit
EOF

You can find lot of much more complex examples for Workflows, Trackers, Users, Groups etc in test/functional/ directory.