I've taken a small detour from my regular game development objectives to concentrate on improving the game controls to respond to a lot of requests to make them less confusing. It's quite insane that the controls have been almost the same since development began, at least when it comes to the mouse button designations for most of the primary commands.
Get Dungeon Colony Early Access Now! Version 0.2.0.96
The old commands used to select units and object with the left mouse and command them using the right mouse. This also applied to items in an inventory: You would select left and move (in or out of inventory) using the right mouse. This wasn't very intuitive given the difference between units and objects that can be selected on the map.
The new controls are mostly completely left click: Please give it a try and let me know if there is anything you would change.
If you are already familiar with the old controls or like the controls just the way they were then you can go back and switch between them in the updated Settings menu:
On the left is a new column for "Custom Controls". Here you can switch between the left/right mouse control settings. Any future customizations will be added to this area.