Ignoring .git/.hg files

Finally Got CoronaViewer working after a couple of days of frustrations! 

Now I am running into minor problems, the most irritating being Dropbox unable to sync files with just extensions(.git for example). Selective Sync in Dropbox is available only for folders, so we are unable to ignore the files as well. 

I found a hacked solution online (http://superuser.com/a/757498/137962) but it looked really ugly (we’d probably use it as a last resort). 

We use Mercurial for version control, so a lot of .hg* files are created.  With Dropbox unable to sync them, we had to maintain separate folders for our project(one for the actual coding, one for CoronaViewer), which seems highly inefficient. 

This is actually a Dropbox problem, so no point in blaming CL.
I just want to ask if anyone else has faced similar problems… 
And if yes, how did you overcome this?