Add missing template instanatiation in Java bindings
Java bindings improvements for CASCADE, minor cleanup.
General pre-release cleanup commit

* Rename {model,util_model}.{h,cpp} files to match class names
* Fix alreadyVisited() issue in TheoryEngine
* Remove spurious Message that causes compliance issues
* Update copyrights, fix public/private markings in headers
* minor comment fixes
* remove EXTRACT_OP as a special-case in typechecker
* note about rewriters in theoryskel readme
* Clean up some compiler warnings
* Code typos and spacing
Fix for compile error when using gcc 4.7 with -std=gnu++11.  Thanks to Martin Brain for the patch!
Ignore config/compile file, which newer autotools create
Fix portfolio compile error.
Fix proofs build.