HSBNE Maintains a number of RepRaps, this repo allows versioning and tweaking of their configs.
RepRapName/
|- ConfigurationName/ (ie Default;Fast;HighQuality)
|- configfile.something (ie slic3r, SFACT, Pronterface, Repetier etc)
Stick to whatever convention is detailed above, feel free to suggest a new structure.
If you wish to modify an existing configuration, please attach a comparison photo of before/after to prove your changes are beneficial.