Running the IG Publisher (current build as of today, 10 Apr 2019) on a DSTU2-based IG without cached packages results in the following error:

Installing hl7.fhir.core#1.0.2 to the package cache
Fetching:............................................................................................................
......................................................................................................................
......................................................................................................................
..............|
Analysing.............................................................................................................
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........................................................................................................... done.
Load hl7.fhir.core-1.0.2 package from /Users/cmoesel/.fhir/packages/hl7.fhir.core#1.0.2 (15.0736sec)
Publishing Content Failed: Unknown FHIRVersion code '1.9.0' (19.0107sec)
(19.0108sec)
Use -? to get command line help (19.0108sec)
(19.0108sec)
Stack Dump (for debugging): (19.0108sec)
org.hl7.fhir.exceptions.FHIRException: Unknown FHIRVersion code '1.9.0'
at org.hl7.fhir.r5.model.Enumerations$FHIRVersion.fromCode(Enumerations.java:10015)
at org.hl7.fhir.convertors.VersionConvertor_10_50.convertStructureDefinition(VersionConvertor_10_50.java:10262)
at org.hl7.fhir.convertors.VersionConvertor_10_50.convertResource(VersionConvertor_10_50.java:12096)
at org.hl7.fhir.convertors.R2ToR5Loader.loadBundle(R2ToR5Loader.java:58)
at org.hl7.fhir.r5.context.SimpleWorkerContext.loadFromFileJson(SimpleWorkerContext.java:259)
at org.hl7.fhir.r5.context.SimpleWorkerContext.loadDefinitionItem(SimpleWorkerContext.java:211)
at org.hl7.fhir.r5.context.SimpleWorkerContext.loadFromPackage(SimpleWorkerContext.java:288)
at org.hl7.fhir.r5.context.SimpleWorkerContext.fromPackage(SimpleWorkerContext.java:157)
at org.hl7.fhir.igtools.publisher.SpecificationPackage.fromPackage(SpecificationPackage.java:44)
at org.hl7.fhir.igtools.publisher.Publisher.loadPack(Publisher.java:1532)
at org.hl7.fhir.igtools.publisher.Publisher.loadCorePackage(Publisher.java:1501)
at org.hl7.fhir.igtools.publisher.Publisher.initializeFromJson(Publisher.java:1135)
at org.hl7.fhir.igtools.publisher.Publisher.initialize(Publisher.java:984)
at org.hl7.fhir.igtools.publisher.Publisher.execute(Publisher.java:555)
at org.hl7.fhir.igtools.publisher.Publisher.main(Publisher.java:5172)
Exception in thread "main" java.lang.NullPointerException
at org.hl7.fhir.igtools.publisher.Publisher.main(Publisher.java:5182)

To reproduce this, simply rename your $USER/.fhir folder to something else (so the publisher has to rebuild the cache). If you already have a previously cached package, this stack trace does not appear.