Jalview quits immediately after starting up with 'URI is not hierarchical' error

Build appears to be broken (commits until Merge branch 'bug/JAL-1734_misleading-progress-bar' into develop), so the following may disappear once issues resolved.

Symptom: launch jalview develop via JNLP, jalview launches then java shuts it down with the following Java Web start launch exception;

java.lang.IllegalArgumentException: URI is not hierarchical
at java.io.File.<init>(Unknown Source)
at jalview.io.BioJsHTMLOutput.syncUpdates(BioJsHTMLOutput.java:222)
at jalview.io.BioJsHTMLOutput.updateBioJS(BioJsHTMLOutput.java:189)
at jalview.bin.Jalview.main(Jalview.java:229)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(Unknown Source)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(Unknown Source)
at java.lang.reflect.Method.invoke(Unknown Source)
at com.sun.javaws.Launcher.executeApplication(Unknown Source)
at com.sun.javaws.Launcher.executeMainClass(Unknown Source)
at com.sun.javaws.Launcher.doLaunchApp(Unknown Source)
at com.sun.javaws.Launcher.run(Unknown Source)
at java.lang.Thread.run(Unknown Source)