@mmunoz2 Can you clarify what it is you're asking here? Do you mean what directories are checked for installed applications? Or just any directories checked during a recon in general? If you mean the former, that is controlled by your inventory collection settings in the JSS, under Management Settings >> Computer Management >> Computer Management Framework. Its in Inventory Collection, then Software > Applications.
If you meant overall what is checked with a recon, well, can't say I really know for sure. I'd imagine it checks quite a few locations all around the drive by way of different built in commands, since it needs to collect things like the OS version, package receipts, cached software, printers and so on and so on.