Intake, in this case, describes the amount of prisoners arriving each day and their regularity, or if they arrive at all.
As of Alpha-2 a new option was created to control the 'Intake' (or 'Continuous Intake') of prisoners. Two options are now available at the creation of a new prison:
If you have the continuous option enabled, the game will behave the same as Alpha-1, prisoners will arrive every morning in various quantities. However, they will never exceed 24 prisoners per day (Fixed in Alpha-2).
If you have continuous intake disabled then prisoners will only arrive if you have room for them. This becomes extremely handy when you want to focus on creating a big prison without prisoners getting in the way. Only partition cells when ready to receive prisoners, then the next day "X" amount of prisoners will arrive to full your prison to max capacity. Intake can also be disabled for the specific Risk Levels of Prisoners if you want to reject intake of Maximum/High Risk prisoners, for example.
Even if you have continuous intake disabled, when you first start your prison, as of Alpha 10, you will still see prisoners incoming. This is because the 'Normal' prisoners are set to open in your Regime.
Go into the Regime, go to Prisoners, and set 'Normal' prisoners from 'Open' to 'Closed'. You will not see any prisoners come in until you turn it back on.
If you turn one of the categories of prisoners on, the clock will start as if it was never turned off - meaning you can turn it off in the early morning, and have prisoners arriving within the hour.