Fix indent in built-in sources
Minor, update outdated deprecation comment
Rewrite mutable collection stub method generation

The main problem of the previous approach was that we were only generating
erased method signatures, which was incorrect in case a class also had a member
from another supertype with the same signature as the substituted one from the
collection. Javac issues compilation errors when compiling Java code against
such classes.

Also all the needed method stub signatures were hardcoded in
generateBuiltInMethodStubs() and the case of MutableListIterator was missing