Apply the use_packages option per file

Previously the package name was applied/prepended after all imports
had been processed and merged, but before resolving names.

But the package statement is per file, so the use_package option must
apply per file, meaning that package names must be prepended per file
rather than after all imports have been processed and merged. This is
now done this way.

The following proto files previously failed to compile, but now
succeed:

   a.proto:

      package a;
      import "b.proto";

   b.proto:

      package b;
Add a command line option, -pkgs, for use_packages
Prepare for 3.17.3