Add ability to change CV & Q phases

Add the ability to input phases for both the length-at-age CV parameters (young and old) and the catchability parameters (Q) for the Survey and the CPUE. If any of the inputs are NULL then the phase is left at the default value specified in the ctl file.
Add ability to change CV & Q phases

Extend the function of the change_e arguments to change the phase in which the CV and Q parameters are estimated.
extend change_e arguments
extend change_e arguments
extend change_e arguments
correct change_e making naming more specific
update change_e args

Include arguments for the new change_e. Specifically turn off the catchability parameter for the CPUE.
natM_phase should be estimated in E0
natM_phase should be estimated in E0
natM_phase should be estimated in E0
change_e make grep names more generic

Generalize the character values called by grep so that if the names of the survey and CPUE are not exact the function does not fail to operate. This will enable using the full capabilities of change_e on the example "run_ss3sim_eg".
Create E2-cod.txt
Create E2-fla.txt
Create E2-sar.txt
natM_phase should NOT be estimated in E0

I was wrong on my last edit. I do not know how to go back to a previous file before the wrong commit. So I am changing it again. Sorry Sean.
natM_phase should NOT be estimated in E0
natM_phase should NOT be estimated in E0
Update E2-cod.txt
Update E2-fla.txt
Update E2-sar.txt