Can I export the SNPs between whole genome alignments using the command line?
It works for me with the download from download page. The download archive contains Mauve.jar so the command line in the answer you link to should work.

However, you might need to include all the jar files (not just Mauve.jar) in the classpath for this to command work, though. For instance, the following works for me:

MAUVE_DIR=‹the-dir-containing-Mauve.jar›
export CLASSPATH="$(find "$MAUVE_DIR" -name \*.jar -print0 | tr '\0' :)$CLASSPATH"
java org.gel.mauve.analysis.SnpExporter -f aln.xmfa -o aln.snps


… there’s probably a smarter way to make this work but I don’t use Java enough to know how.