When you go to ballot, or any form of publication for a FHIR IG through HL7, you have to provide an XML document that defines the pages and artifacts that the HL7 Jira system will use for reporting issues or comments on the specification.
If you are smart, you create an initial template in the HL7/JIRA-spec-artifacts page when you start your project. If you aren't, you wait a while and then create it.
The initial version should look something like this:
<?xml version="1.0" encoding="UTF-8"?>
<specification
gitUrl="https://github.com/HL7/fhir-project-mhealth"
url="https://hl7.org/fhir/uv/mhealth-framework"
ciUrl="http://build.fhir.org/ig/HL7/fhir-project-mhealth"
defaultWorkgroup="mh" defaultVersion="0.1"
xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
xsi:noNamespaceSchemaLocation="../schemas/specification.xsd">
<version code="0.1"/>
<artifactPageExtension value="-definitions"/>
<artifactPageExtension value="-examples"/>
<artifactPageExtension value="-mappings"/>
<page name="(NA)" key="NA"/>
<page name="(many)" key="many"/>
<page name="(profiles)" key="profiles"/>
</specification>
But you will need to add lines for each artifact (Profile, ValueSet, et cetera) and page (.md or .html file) that you generate.
<artifact name="Artifact Title"
key="artifact-id" id="artifact-filename-without-extensions"/>
<page name="Table of Contents" key="toc"/>
This can be awfully tedious, but the IG Publisher can create an updated one for you, although if you haven't created one in JIRA-spec-artificact, for some reason it doesn't seem to create an initial one for you. I'm not clear on why it doesn't, but I found a workaround.
What you do is create that initial version, and copy it to your templates folder, naming it jiraspec.xml. Then you run the IG Builder without a vocabulary server.
C:\myproject> JAVA -jar "..\%publisher_jar%" -ig ig.ini -tx n/a
Telling the IG Builder that you don't have a vocabular server makes it assume that you do NOT have an internet connection, and so it also doesn't try to get your templates or copy the current JIRA Spec over that file I had you create above. Now when you run the IG Builder, it will create an initial JIRA spec file for you, which you can then generate a pull request to https://github.com/HL7/JIRA-Spec-Artifacts/xml.
Once you've finished, you can find the created specification in your project in template/jira.xml, which you can then rename appropriately and send a pull request to the JIRA-spec-artifacts page.
Ideally, this specification configuration could be more automated in a FHIR IG Build, but for now what we have works. It's just a bit of a pain.