Addressed many of the concerns of bug 10 (build system code review).

Addressed many of the concerns of bug 10 (build system code review).
Some parts split into other bugs: 19, 20, 21.

Addressed concerns of bug 11 (util package code review).

Slight parser source file modifications: file comments, #included
headers in generated parsers/lexers

Added CVC4::Result propagation back through
MiniSat->PropEngine->SmtEngine->main().  Silenced MiniSat when
verbosity is not requested.