Libraries

This is already a widely discussed topic:
#1852332: Integrate with the Libraries API module
#1838982: twitter_bootstrap_ui module

A few alternatives also exist:
http://drupal.org/project/twitter_bootstrap_ui
http://drupal.org/project/bootstrap_api

Ultimately the problem with putting the Bootstrap framework in a libraries path instead of the sub-theme is that it makes it hard to include the bootstrap source files (.less files) to take advantage of change the variables, using mixins and compiling it all together.

If you're just looking for using the standard bootstrap framework and overriding the CSS only where needed you can use the Bootstrap CDN option. This is also better explained in the new starter-kit sub-theme that was added in #1844448: Add sub-theme starter kit.

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