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JSHint 2.2.0 supports an "ignore" statement which can be used to wrap blocks of code which should be passed over by the linter.
/* jshint ignore:start */ <div><span></span></div> /* jshint ignore:end */
I feel this is a much better solution than transforming and wrapping JSHint with a series of transforms since the code produced by JSX's transpiler might produce code which does not comply to your internal lint/hint guidelines.
If you feel you need to use a wrapper around JSHint and want to have JSHint run on your transformed JSX code, please see STRML/JSXHint