When I run the jsdox command recursively on a directory, debug shows that it's processing .txt, .json, and other file types. When those file types are hit, jsdox bails out with an exception, which means I can't recursively generate documentation.
It should allow a file mask (I've not seen an example supporting this). The jsdox website claimed a recursive directory parse would only pick up .js files, but apparently that's untrue.