Any added prefixes are now used *after* all input files have been
parsed to look for a prefixed, flattened version of the input file
somewhere in BROPATH and, if found, load it.
For example, if "lcl" is in @prefixes, and site.bro is loaded, then
a file named "lcl.site.bro" that's in BROPATH would end up being
automatically loaded as well. Packages work similarly, e.g. loading
"protocols/http" means a file named "lcl.protocols.http.bro" in BROPATH
gets loaded automatically.