Fix locally colliding persistence folders for SW repository and SW cache. Refactoring.
* induce configuration by Properties to HostRuntime and SoftwareRepository
* add configuration parameters for persistence folders (to be tested)
* refactor SystemProperties to PropertyReader to make it usable with other Properties sets

relates to #97
Merge branch 'socketworks' of github.com:radek-macha/everBeen into socketworks

Conflicts:
	been-api/src/main/java/cz/cuni/mff/d3s/been/api/BeenApiImpl.java
	host-runtime/src/main/java/cz/cuni/mff/d3s/been/hostruntime/ProcessManager.java