Automatic mode is a term invented by this wiki. It describes the condition of using replace.py, and some other scripts, in such a way that you do not have to approve each change proposed by the bot. This mode might also be described as running the bot in an "unattended" way.
It is the opposite of manual mode, in which you have to answer the following question (or one like it) to apply the proposed change:
Do you want to accept these changes? ([y]es, [N]o, [e]dit, open in [b]rowser, [a]ll, [q]uit)
To enter automatic mode, chose the [a]ll option. Your changes will then be applied without your individual approval. Automatic mode can also be attained through the use of the -always parameters in most scripts.
You are strongly advised to always use manual mode — and therefore never choose "[a]ll" — until you are sure that your proposed changes will be applicable in every situation. Put another way, always use manual mode when there's a possibility that your code may allow an undesirable number of false-positives.