Getdown launcher does not work first time when using an appbase with a different set of resource/code files (e.g. jars).

When using a .jvl file to launch Jalview which contains a new appbase, if the getdown folder at the new appbase does not contain the code and resource items found in the original appbase (i.e. the one that the Jalview instance had before clicking on the .jvl) then Jalview fails to launch.

This seems to be because the list of files needed to download (resource and code values in the original getdown.txt) gets added to by the getdown.txt in the new appbase location, not replaced. This means that if some files in the original getdown.txt have changed name (e.g. a jar upgrade) or are otherwise just not there then getdown cannot find those files and decides (after trying 5 times for each file) not to launch.

Quitting Jalview and clicking on the jvl file again will then succeed because the new appbase getdown.txt is now in place.

Fix what happens when clicking on the jvl file the first time.

By implication, the release channel will display this same error if a file is moved/renamed or otherwise no longer available. This could be managed (e.g. leaving all old files in place but dropping them from the getdown.txt lists).

2.11.0 has the same set of files as 2.11.1.0 so the problem does not arise between these versions.

This bug blocks advertising the archive version jalview.jvls.