Manually fix/comment classes to pass compilation

- Annotations and java.lang.Object are commented out.
- Most errors are due to either wrong number of argument/type in
  constructors, duplicate methods after type erasure or illegal visibility
  refinements.
- The following 5 classes crash the compiler when placed in the java
  package and are moved to fixed.java:

java.lang.InterruptedException.scala
java.io.UnsupportedEncodingException.scala
java.lang.CloneNotSupportedException.scala
java.lang.String.scala
java.lang.Throwable.scala
Move signatures to match standard package structure