New guide --include-dir clarifications

[Nir Lisker]

Hi,

A couple of points regarding --include-dir in the guide that I think are
worth mentioning:
1. The directories are searched in order, so if the same header is found in
more than one included dirs, only the first one is taken. (I think this is
correct.)
2. The directories are *not* searched recursively. Nested directories need
to be added one by one if required.

If you agree that these should be added, I don't mind making a pull
request. I think it's best to add this info in the "Running jextract"
section.

- Nir
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