{dirname} substitution always substitutes the absolute dirname

When running jalview's new command line with a {dirname} subsitution in the output, "{dirname}" is replaced with the full path of the input file's directory, even if the opening path relative. e.g.

jalview --open examples/*.fa --output tmp/{dirname}/{basename}.stk

you would expect/want to save files in
  tmp/examples/
but it tries to save in
  tmp/Users/BSoares/Work/git/develop/jalview/examples/
which is unlikely to be the intended target.

The command line opener converts relative paths to full paths which is why this is happening, but it could remember the original relative path to use for the substitution.

Could also add a --mkdirs bootstrap arg to ensure deep folders are made (with appropriate warning/info when they aren't).