I recently downloaded the mCODE JSON definitions from here:
http://hl7.org/fhir/us/mcode/STU1/definitions.json.zip

And what I found is that much of the generated XHTML content in Narrative text contain template URLs that looks like this:

<a href=\"{{[type]}}-{{[id]}}-definitions.html#Observation\">Observation</a>

This causes validation errors:

Unable to add: StructureDefinition-mcode-karnofsky-performance-status.json to the index due to exception: Invalid XHTML content: cvc-datatype-valid.1.2.1: '{{[type]}}-{{[id]}}-definitions.html#Observation' is not a valid value for 'anyURI'. [StructureDefinition.text]

The JSON definitions that are inline on the spec website don't appear to have the same issue. I'm guessing that there is a find/replace step that didn't happen in generating the JSON definition package.

I also tried downloading the full IG site and the definitions.json.zip file contained within that also has the issue.

Is this a tooling problem?

URI uri = new URI("{{[type]}}-{{[id]}}-definitions.html#Observation");

yields the following exception:

java.net.URISyntaxException: Illegal character in path at index 0: {{[type]}}-{{[id]}}-definitions.html#Observation

The URI parser doesn't like curly braces or the square brackets. Escaping them using the proper character entity references seems to alleviate the problem but I think the fix is that these values should be replaced with the actual type and id values that were intended.

The downloadable XML definitions suffer from the same problem.

I also found an issue with an Id value in the ImplementationGuide resource itself:

Unable to add: ImplementationGuide-hl7.fhir.us.mcode.json to the index due to exception: Id value: '_str_abstractprofile' contain invalid character '_' [ImplementationGuide.definition.resource[0]]