Updates required for BASE 3 support + use new features

[Nicklas Nordborg]

Need to make some packaging changes. Build script changes needed since BASE jar file have different names. See the net.sf.basedb.examples build script for ideas.

Verify that the code works with BASE 3.

Use new features in BASE 3. Subtypes of items (​http://base.thep.lu.se/ticket/1597) should be very useful for Reggie. Eg. we can define item types Patient, Case, Specimen, etc. and use those items types for filtering when searching for existing information. No more pattern-matching problems like #324.