Here is the explanation about the word "indenture":

An Indenture is a legal contract between two parties, particularly for indentured labour or a term of apprenticeship but also for certain land transactions. The term comes from the medieval English "indenture of retainer" — a legal contract written in duplicate on the same sheet, with the copies separated by cutting along a jagged (toothed, hence the term "indenture") line so that the teeth of the two parts could later be refitted to confirm authenticity.
My impression is that every object in the big country houses was catalogued, so I think that the rental contract must have been very detailed and huge. How many clerks would Mr. Shepherd have to work on that single contract?
It is strange that Elizabeth cares about plants; I read this as Elizabeth making sure her exotic plants are propagated, in case some did not survive the absence of Elizabeth's tender loving care ;-). I imagine Elizabeth showing off her fashionable plants to visitors.