+ MISO-4 Implemented changes required to support a single miso.baseDirectory configuration that is then used in relevant other configurations, e.g. ehcache diskstore path, logging directories, etc

+ Enforced the UTF-8 build encoding property for all compilation profiles. This should hopefully fix some of the regex compilation wierdness with non-English alphabets (thanks Sven!).

+ Rapid-run mode HiSeq notification was not picking up correct run status thanks to log file modifications. Thanks Illumina.