Unless otherwise specified, Bower will download the latest release from your repo.
If you have not created a new version yet, it will appear that Bower is loading from the original Github branch. The latest version of your forked repo is the same as the original.
One option is to create a new version for the forked repo, and it should work as expected.
Or you can use bower install http://my_custom_url.git#commit , where commit is the name of the last commit with your changes to the Bootstrap code.
You can use branchname instead of commit , but then you risk changing the code without understanding it.
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