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.
Switch to using an iterator to avoid raw types / unchecked conversion warnings.
Upgrade libraries:
 - httpclient from 4.2.5 to 4.3.3
 - httpcore from 4.2.4 to 4.3.2

Both changes will be used in a later commit to add CT log retrieve
functionality to the Java client.
Use the protobuf jar file from the system.

Either sysjarsdir or jars.protobuf can be overridden in local.properties.
Add support for a Travis continuous build.