Kevin,
The inst/ directory gives a good handle to pass arbitrary directory layouts
of your choosing through. You just need to avoid inst/data as it would clash
with an existing data/ directory.
I think I have seen
inst/rawData
inst/extData # as in 'external data'
and of course
inst/scripts
or
inst/tools
Note that there is a reasonable discussion in Writing R Extensions, but as
always, you have to find it first.
Dirk