Read :h :helptags, this command (with an argument:) is :Helptags /path/to/dirused to index the documentation of a third-party plugin. This has nothing to do with the Syntastic plugin.
If Pathogen is installed correctly, it :h syntasticshould open the documentation for Syntastic. Read carefully, make sure that you understand everything, try and return to us if you have any questions.
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