Fixed issue with custom project properties not taking effect.

Resolved issue with not being able to set custom
project properties by moving addCompileProtoTask and addSourceJarTask
calls into project.afterEvaluate.

Added a new project property "outputToProjectDir" for outputting
generated files relative to project root directory instead of relative
to build directory.

Bumped version number to 0.4.0 since it is a patch for a bug and adds a
new configuration option.
Whitespace cleanup.