Water closets are cleaned by flushing water that usually enters a main sewer or more rarely a septic tank.
A rarely-surviving variant on the water closet is the tippler. Waste eater from the house was piped into a pivoted cast iron tank which when full to a certain level automatically tipped over and flushed the outside toilet.
Earth closets, often called privies, stood over a hole or cesspit and these had to be dug out periodically. In the countryside this accounted for the rich soil in cottage gardens, but in cities they led to health problems. Nightsoil men would be hired to dig out and cart away the sewage.
In some towns a system of back-yard 'bucket' toilets was used. This may be the type referred to in your document but I haven't ever heard the phrase 'Jacob's boxes' before. This was a system of standardised galvanised metal tubs. A tub sat under the loo seat. Hopefully frequently, the nightsoil men would remove these through a special low hatch and empty them onto their cart. Aka honeybuckets.
Nightsoil - on account of this offensive activity being done at night so as to make use of the quieter streets and fewer people.