When using a plist, take relative paths in --index-desc and --include as relative from plist location

Anything in the --input section of a plist is taken as relative to the plist's location, using something like

```
[self combineBasePath:plistPath withRelativePath:inputPath];
```

However, this doesn't appear to be applied to things passed in via --index-desc and --include. I think it should be.
