[Avida-cvs] avida/current/source/main CVS commit

[Dr. Charles A. Ofria]

Update of /cvsroot/avida/avida/current/source/main
In directory usw-pr-cvs1:/tmp/cvs-serv27134/main

Modified Files:
	phenotype.cc phenotype.hh 
Log Message:
* Fixed calculation of base merit in test CPUs (It was always using full size,
  no matter what was set in genesis)

* Removed instruction flags for crossover mutations and added an inject
  flag.  The inject flag marks each instruction that is injected into one
  organism by another.  We can always bring crossover flag back if we need
  it later.

* Setup the IsModified flag to be set when code is injected into a genome.

* Fixed some class names to get avida to compile with threading turned on.