The name given to the routines established between Mama and the kids, where Mama and the kids know what procedure is happening when they say, for example, "Pick me up after Fine Arts Camp", when the time window is any time that day after the camp lets out at five, and there are at least three valid parking lots to be picked up from. Mama and the kids know that the usual procedure is right at five in the tiny cramped parking lot by the music and art wing, the one with all the reserved spaces for the symphony and staff, but FatherSir, having been told only that there is to be a pickup of kid, and he's the one to do it, is clueless and haunting the wrong parking lot.
The construction "The secret protocols of foo" applies to any situation where the protocol is sufficiently well-known by insiders that it's not thought to clue in the outsider who's expected to follow the protocol.