fixed bug in crctx
fixed simulation initialization. Previously initializing built agent instances from the db used prototype cloning followed by initfrom(db).  This resulted in some initialization potentially being done twice.  Fix changes init procedure to initialize built agent instances raw via DynamicModule. Also a minor fix to crctx
Merge pull request #805 from rwcarlsen/init-fix

simulation initialization fix
updated greedy preconditioner documentation
adds a test and implementation check for empty preferences
Merge pull request #810 from gidden/empty-req

adds a test and implementation check for empty preferences
Move files from integration_tests dir to tests dir.
Suppress cycpp pass 3 tests and rename another file to avoid nosetests.