Running test/run.sh -s still appears to do the melt:
[INFO] Generating build scripts
[INFO] Skipping the build; run melt.sh to do it.
[INFO] Melt complete: /home/hinerm/code/pom-scijava/target/mega-melt
Adjusting melting pot build script... Done!
Melting the pot...
the melting-pot.sh script appears to skip the build appropriately (Skipping the build; run melt.sh to do it) but the somehow melt.sh runs anyway (Melting the pot...)