Handle relative paths in JVL files

JVL files containing command line arguments that refer to paths relative to the location of the JVL aren't handled correctly when opened by double clicking the JVL file in the OS's native file browser tool (chooser, explorer, etc).

for example create a JVL file in the jalview git repo's 'examples directory':
```
% cat > pfdx.jvl <<JVL
jalview.apparg = --open plantfdx.fa
jalview.apparg = --features plantfdx.features
JVL
```

and on a mac:
```
open -a ~/Applications/Jalview.app pfdx.jvl
```
   
Jalview opens, processes the JVL but fails to open the alignment or add features.