Revise packet-gathering loop in scan_incoming

Revise packet-gathering loop in scan_incoming

Since every packet must contain a directive, the process is now driven
based on the set of directives available.  This change also avoids
considering every file and fixes a related minor bug in the old code:
comments indicated that all files from each triplet were supposed to be
removed from possible consideration, but the loop was actually iterating
over a temporary list containing the keys of the %possible hash as of the
start of the loop.

This change also introduces a new internal format for the result of the
scan_incoming function and some temporary scaffolding code to convert the
new format to the old format to keep the tool working during the change.