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Make Your Own Custom Build of Bootstrap Using Less to Generate new CSS

http://bootstrap-live-customizer.com/
THE best Bootstrap customizer tool on the web. You can view the changes live. Very thorough. When done, it generates the new less and css files you need.

Found the live customizer tool on this blogpost:
http://blog.codeinside.eu/2014/11/18/Easy-Ways-To-Customize-Bootstrap/

The official bootstrap site provides bootstrap custom builder to generate your own custom build of bootstrap. Also they provide the less and sass version of the files for you to work and compile the css file to suit your requirement. But those options are not for everyone and you should keep track of all the changes you have made going in that way. Also it gives you a headache in case you want to upgrade to higher versions of bootstrap later.

Other Builders

http://stylebootstrap.info/
http://pikock.github.io/bootstrap-magic/