Ugh, sorry I'll try to remember to mention OS X/Linux in the future when talking about save compatibility. Just didn't occur to me; was only thinking about whether old saves would be compatible, not what you'd need to do to transfer them over on OS X.
Would it be possible to move the saves folder into a library/application support/fractalsoftworks folder?
This is the industry standard way of placing saves on OSX and would prevent this from happening in the future.
The same with Windows tbh; saving in the game's installation folder is really bad practice. (completely ignores user access rights, and multi-user environments)
Likewise, mods shouldn't be where they are either.
Though what's considered 'good practice' depends upon who you ask.
Many games write save game data to "%UserProfile%\Documents\My Games".
Yet typical application data should be placed in "%AppData%".
Then there's "%UserProfile%\Saved Games", which seems the most appropriately named folder, yet very few games actually use this location.
The only constant, is that there's no convention for name-spacing your game's folder.
Some games use \Publish\Full Game Name".
Some use just "\Full Game Name"
Others use "\AbbreviatedGameNameInCamelCase".
A right royal f**king mess if you ask me.
Steam's \SteamApps\ folder is equally slapdash & lacking any kind of convention, though at least that's all governed by a central authority. (Valve)
It all makes the simplicity & durability of Java's name spacing convention (reversedCompanyDomain.package.Class) look positively idyllic.