Fixed issue with default project properties overwriting custom project properties.

Resolved issue with default project properties overwriting custom
project properties by moving addCompileProtoTask and addSourceJarTask
calls into project.afterEvaluate.
Bumped version number to 0.3.1.
Added project property for outputting generated files relative to project
directory instead of relative to the build directory.
Merge branch 'master' of https://github.com/trulsmag/gradle-protobuf-plugin