fix bug 534: portfolio define-fun duplicate model
Documentation fixes, some code typo fixes, file perms, other minor things.
Move some regress benchmarks around that took too long, other test cleanup.
Fix sat_proof "parentheses into the void" after conferring with Liana.
Change default option of simple ite lifting within quantifier bodies.  add some debug messages.
Fix (extraneous) command dumping.
Fixes to theoryof-mode; no longer static in Theory class.
Support for bv2nat/int2bv in parser and BV rewriter.
Support a personal build configuration and make rules.
Fix for bug 528
Cleaner version of bug-fix for 528, also moved substitutions.h out of theory.h
for faster compilation