Manual 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 have to approve each change proposed by the bot. It is the opposite of automatic mode, in which the bot is allowed to run unattended.
In most scripts, manual mode is the default condition. It prompts you with the question:
Do you want to accept these changes? ([y]es, [N]o, [e]dit, open in [b]rowser, [a]ll, [q]uit)
and requires you to choose from the options provided.
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.