I think (i may be wrong) that flashdevelop "references" are just autocompletion and not actually passed to the compiler.
I'm not sure what's the "right" way to do it, but I can tell you what I've done (I made a few helper classes for flambe too :P): I simply created a "fake" haxelib, I created HaxeToolkit/haxe/lib/[name]/git, and in [name] i created a .current file that contains "git".
Then on flashdevelop you have to add it as a library (Project settings -> Compiler options -> Libraries).
Note: there are probably other/better ways to do it.