Extensions with latest ScalaBuff version

Hi,

this pull request contains a variety of extensions for compatibility with the latest ScalaBuff version.

(1) Upgraded default ScalaBuff version to 1.3.9.
Currently, only 1.3.8 is out, but that version seems ambigous (i.e. changes were made to 1.3.8 without version bump -> pull request to create ScalaBuff 1.3.9 is pending)

(2) upgrade to Protobuf 2.5.0 (in acc. with ScalaBuff, Akka, and most other libs)

(3) changed output folder to plain source-managed (better IDE integration)

(4) changed input of protos - instead of processing individual protos, let ScalaBuff process entire folder via --proto-path param (includes between protos do not work otherwise)

cheers,
-Tom