Old Tom made many modifications to The Old Course from 1865 to 1904. Before Old Tom, perhaps with the exception of Allan Robertson the Old Course had evolved over the years. But major changes occurred under Old Tom, by rights he modified the course, however if you modify something, then you have change the original design concept – which can be interoperated as a new design - therefore saying Old Tom designed the Old Course would not be incorrect, however I prefer to say he modified the course on many occasions over the years.
Ian is right to mention the earlier holes; from memory, I believe that the course had only 10-12 holes in the 18th Century. My father mentioned that a couple of holes had been located either on the site of R&A Club House or behind it leading up to the Martyrs’ Monument – today the area is call The Scores (see attached photo – note Monument between R&A Club House & Hamilton Hall - the red building to RH side) – although near but not quite on the same position as Ian mentioned. The 1st and 18th Greens are new greens created by Old Tom. Land was reclaimed from the sea (West Sands) and I understand that Old Tom built the 1st Green on this reclaimed land around 1870. The road which runs behind the R&A Club House – the section that starts at the end of the Golf Museum through to the West Sands is all reclaimed from the sea.
As for whins, heathers and dune grass etc, this was removed to improve the course, however some say that this was not by Old Tom but by nature -interesting that only areas around the Old Course seem to have died back, leaving others adjacent areas in reasonable health. Interesting point, perhaps someone up there likes golfers?