Remove the app-layer-PROTO stub for Rust based parsers. It is no longer
needed as Rust parsers now contain the registration function in Rust.
Ticket: 4939
adjust lines for patching /src/Makefile.am, as current generated
Makefile wasn't building Suricata.
Add suggestion to run "./configure" before running "make".
Add --logger and --parser options to examples.
The idea being that it is easier to read and maintain than
wrapping ed commands.
This script also merges the parser and logger setup into a single
script, but still allows just the parser, or just the logger
to be generated with flags, --logger and --parser.