{
    "tags": {
        "allowUnknownTags": false
    },
    "source": {
        "exclude": [],
        "includePattern": ".+\\.js(doc)?$",
        "excludePattern": "(^|\\/|\\\\)_"
    },
    "plugins": [
        "./tsd-jsdoc/plugin"
    ],
    "opts": {
        "encoding"      : "utf8",
        "recurse"       : true,
        "lenient"       : true,
        "template"      : "./tsd-jsdoc",

        "private"       : false,
        "comments"      : true,
        "destination"   : false
    }
}
{
    "tags": {
        "allowUnknownTags": false
    },
    "plugins": [
        "./tsd-jsdoc/plugin"
    ],
    "opts": {
        "encoding"      : "utf8",
        "recurse"       : true,
        "lenient"       : true,
        "template"      : "./tsd-jsdoc",

        "private"       : false,
        "comments"      : true,
        "destination"   : false
    }
}

Remove exclude and include patterns from jsdoc config
CLI: Remove exclude and include patterns from jsdoc config

