JalviewJS runtime path not resolved when when core files are used

Originally reported in https://github.com/jalview/jalview-js/issues/5

JalviewJS deployed under:
/jalview.js/...

page using Jalview is deployed under
/jalview/...

This requires the Info.j2sPath for pages under /jalview/ to be set to '/jalview.js/swingjs/j2s'
If a corefile is used e.g. (jvexamplefile) then some GET urls appear to include the originating URL's path:

e.g.
In the browser console I can see this:
GET http://dev.../jalview.js/swingjs/swingjs2.js
J2SApplet load JalviewJS loadClazz... swingjs2.js:12881:12
J2SApplet load JalviewJS start applet... swingjs2.js:12881:12
J2SApplet exec JalviewJS loadClazz null -- OK swingjs2.js:12832:12
GET http://dev.../jalview.js/swingjs/j2s/core/corejvexamplefile.z.js
J2SApplet exec JalviewJS start applet null -- OK swingjs2.js:12832:12
JalviewJS loaded /jalview.js/swingjs/j2s/core/corejvexamplefile.z.js:3134:51
JalviewJS running jalview.bin.Jalview /jalview.js/swingjs/j2s/core/corejvexamplefile.z.js:3134:51
GET http://dev.../jalview//jalview.js/swingjs/j2s/sun/util/resources/CalendarData.properties
GET http://dev.../jalview//jalview.js/swingjs/j2s/sun/util/resources/CalendarData_en.properties