Carpenters have always left their mark (figuratively and literally) on their work. In the early nineteenth century, when Samuel Plumb’s house was originally built, they made a lot of marks.
Under the so-called “scribe rule” which had been used for hundreds of years, every joint was marked with a system of Roman numerals gouged into the wood. Each mortise was scribed (see this post for a description) to exactly fit one tenon. So every joint between a post and a beam or a stud and a plate was unique. To keep track of which part went with which, each side of the joint was numbered.
After 1830, a new system, called the “square rule” entered into general use which “squared up” the area around the mortise so that standard parts could be used. This was a heck of a lot quicker and marked the beginning of the transition toward dimensional lumber and all-nailed construction that accelerated after the Civil War. Isolated examples of square rule framing as early as 1816 have been found in New England as discussed in this link from Historic Barns of Connecticut.
But Samuel Plumb’s carpenters, working in 1812, were still “old school” and marked every joint. Since the joint only went together in one way, the carpenters needed to make sure not only that the numbering matched up but also that the parts were facing the right way. That’s probably what the arrow in the top photo is showing: which side of the plate should be facing out when they fit the studs and joists into it.
The photo below of the roof deck support structure shows another example of this marking system in use. It’s tough to figure out exactly what the “VIII” is marking in this location. It could be number of the ceiling joist next to it (which was pinned to the plate underneath the rafter) or perhaps the number of a mortise (out of view) cut into the plate below to receive a tenon for a support post. Anyway, it’s a “VIII” looking for another “VIII” as its mate.