Calls to Java's primitive class methods work.

Calls to Java's primitive classes that had the same name as the
corresponding primitive in Kotlin didn't work. Now calls like
Short.valueOf() is turned to java.lang.Short.valueOf() in Kotlin.
add Debug mode to run configurations
Fix compilation
Add EntryPointsManager entry to misc.xml

This is always added to the xml when the project is opened. It's
annoying to see this change when you do anything.
Fixes to handling of boxed types

Boxed types and primitive types should cooperate properly now with
primitive types in all basic cases. Added tests that verify this.
Added test case for custom Short class usage
I fixed ArrayWithoutInitializationExpression class for object array and multi
dimension array. And I added 2 tests to check object Initialization.
Fixed an issue with Any? type declarations
Renamed myParamList to starParamList and fixed tests
Convert Java lists to MutableLists

Java lists were given jet.List type, which is incorrect, since Java
lists are mutable and jet.List is immutable. Fixed test cases.
Made foreach work with nullable iterables
add more modifies and tests