The other day, I stumbled upon this question on stackoverflow on how to cleanly customize Bootstrap :
That pushed me to put this workflow on github :
Clone the repository, and you're good to go and customize the variables, mixins and classes of bootstrap while keeping it intact in its own subdirectory. This will allow easy update and keep everything clean.
Under the hood, I created a Grunt task that automatically copy the variables.less file from bootstrap into your less folder while modifying the font path to be correct. This will be done on your first launch of Grunt.
But there is also a default variables.less file in case you don't want to use grunt.