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Until December 2013, if you included non-minified Bootstrap Javascript files in your project, Linguist (the library Github uses to detect languages) would count them towards the Javascript LOC count for your project[0].

I had a number of small web server projects that were incorrectly classified as >95% Javascript for this reason.

Fortunately this was fixed, but I imagine there are a number of other low-hanging fruit that are causing projects to be misclassified as well.

[0] https://github.com/github/linguist/pull/856



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