Added check for zero valid sites

Upgraded doxygen and fixed doxygen comments
Fixed bug in write results
Changed computation order. First H1 then H0
Changed option init H1 from H0 to init H0 from H1
Added maximization forced stop if result does not already pass the LRT
Added MPI trace level and fixed messages
Added testing hooks to BEB.
Passed scale values from H1 to BEB
Fixed relative error default
Added initial map of internal to external site numbers
Changed iterator initialization


git-svn-id: https://svn.vital-it.ch/svn/hp2c/trunk/Codeml_Variants/Fastcodeml@4924 95c5a404-1f88-0410-a6b0-c3f062b6f34a