Add Venafi, Inc. to authors
Moving C++ code to its own subdirectory, adding a top-level Makefile that is
separate from the C++ one.
Fixing IntelliJ repository directory mapping.
Java: Expose warnings when building from the command line.
Organize and sort the .gitignore entries.
Fix up a number of .gitignore entries.

Most of these were caused by c41b090.