Update .gitignore to ignore R history files
Add ability to specify abundance index type

Add the parameter use_index. I have used a switch approach. There are
also some trivial changes to indenting.
Update documentation for use_index option
Remove cast_recruitments code from get_rec_devs

Whether this was present depends on the forecasting settings. By just
grepping for 'F' we avoid this problem. Kelli discovered this bug and
suggested the fix.