removed warnings for oboformat
replaced System.out with log for tools
Removed System.out for tests
removed System.out for oboformat
removed warnings for parsers
Fixes #72 Manchester syntax roundtrip of doubles and SWRL rules fails

Renderer was special casing doubles, but the parser special cases
xsd:decimals.
Test for roundtripping SWRL rules was building variable IRIs with a
different namespace from the renderer default. The result is equivalent
semantically but it looks different and failed the test.