When using a non-standard $wgArticlePath (that is, not /wiki/$1), the automatic process of feeding Wikibase data into the query service will stop working.
The error message when running munge:
0:16:33.843 [main] INFO o.wikidata.query.rdf.tool.rdf.Munger - Unrecognized subjects: [
then follow thousands of statements, all in the form https://artbase.rhizome.org/entity/statement/Q4198-xxxxxx -- then the end of the error:
] while processing https://artbase.rhizome.org/entity/null. Expected only sitelinks and subjects starting with https://artbase.rhizome.org/wiki/Special:EntityData/ and [https://artbase.rhizome.org/entity/]
This is for a wiki that is set up with the $wgArticlePath /$1, according information in the sites table, and a correctly changed .htaccess for Apache to handle the URL routes.
When changing the $wgArticlePath back to the default /wiki/$1, (including switching back information in the sites table and reversing to detault .htaccess) the Munger process completes without any issues.
I am unclear why the Munger would verify siteLinks in the first place (or do any data validation), but if it needs to do that it should check for linked wiki's articlePath, which can be found out using the Mediawiki API.
My suggestion would be to use the existing command line switch --skipSiteLinks to at least not check for the formatting of siteLinks when they're not going to be exported to the query service anyway. At the moment, this switch will prevent siteLinks from being exported, but check their form regardless.
Preferred would be another switch that would make Munger accept any type of siteLink.