Jalview does not honour file format when exporting file as new format via command line

jalview.bin.Jalview.doMain ignores all the flat file output format options listed in its help :
-fasta FILE Create alignment file FILE in Fasta format.
-clustal FILE Create alignment file FILE in Clustal format.
-pfam FILE Create alignment file FILE in PFAM format.
-msf FILE Create alignment file FILE in MSF format.
-pileup FILE Create alignment file FILE in Pileup format
-pir FILE Create alignment file FILE in PIR format.
-blc FILE Create alignment file FILE in BLC format.
-json FILE Create alignment file FILE in JSON format.
-jalview FILE Create alignment file FILE in Jalview format.
-png FILE Create PNG image FILE from alignment.
-svg FILE Create SVG image FILE from alignment.
-html FILE Create HTML file from alignment.
-biojsMSA FILE Create BioJS MSA Viewer HTML file from alignment.
-imgMap FILE Create HTML file FILE with image map of PNG image.
-eps FILE Create EPS file FILE from alignment.

It just writes out the file in the format used to import it.