Options are ignored if default value is `NULL` or `NA`

```
opt('p', 'plotfile', 'file to save plots to', NULL)
```

will always be `NULL`, even if specifying `-p something`

same for `NA`

Start by locating the implementation of opt and reproduce the example with a NULL default, then repeat with an NA default and -p something. Trace how command-line values are compared with these defaults. Done means both defaults accept the supplied option value instead of always returning NULL or NA.

Written by the indexing model from the issue text.