first steps to redesigning repository management to support multiple
repositories
commit progress
add initial native store config
Remove mapPermanentRepository, does not fit with new method
more implementation for serialising and regenerating repository refs

both repository manager and repository references should be able to be
regenerated from the management repository now, which should now be the
only static repository reference for the system
Initialise the repository managers map
make tests compile using a local temporary directory
populate podd home directory in application utils
Make base template configurable
Add test for getting repository twice
fix use of ManualShutdownRepository to be consistent
Support real shutdown for multiple wrapped ManualShutdownRepositories

This avoids accidental bugs causing repositories not to get shutdown
rework to try to avoid issues in reloading tests
test reloading repositories
todo note about checking for the schema in the management repository
work on property support in repository manager
fix log message
add logging for shutdown exceptions
fix javadoc
fixes for bugs identified and logging for other bugs