Thanks for that.
I was sort of leaning towards the #if arduino < 100 option however the readability suffers a lot when you have code that is making use of the changes (eg .write instead of .print changes etc).
I think as there appears to be no real "correct" method that a combination of the below is probably the way to do it with the git branches + downloads being the way to deal with the most "messy" of cases where there's a lot of changes.
Cheers
ajfisher