Automata are the "Artificial Intelligence" that controls the actions of characters during ladder fights , when defending in honor fights, and when using the "R" or "spacebar" command during normal combat. An automaton is a rule matched with an action, with a unique priority level.
Automata are evaluated in the order of the priorities, so the first on top being the highest priority.
There are many types of rules, some are very simple such as "Self" which will always evalutate to True and target the automaton owner by default. Other rules may be more complex, such as "Allies: HP under 70%" which means whenever more than one ally's HP is below 70% of its maximum value, the rule will evaluate to True and target those allies who have HP under 70%.
When a rule evaluates to True, the system will attempt to execute its associated action on the default targets resulting from the rule evaluation. For instance when "Enemy: Weakest" evaluates to true, the default target will be the weakest enemy.
When the action is not valid for the default target, for example if you use the rule "Allies: Dead" in order to cast a defensive spell on yourself, the default targets (dead allies) will be invalid for the defensive spell targeting yourself. The first valid target will then be used, which is the owner since the action is a self spell.
If no target can be found for the action then the rule is ignored and processing goes on to the next automaton node.
Some rules have intelligence and wisdom requirements. So a low intelligence character may not be able to tell weither an ally has 50% HP or 75% HP. In the same vein, a character with high wisdom might recognize symptoms of certain conditions like paralysis and poison, where a less wise character would not.