Clean up warnings in user-example files

[e-perl-NOAA]

See issue #51 in the test-models repos. The models in the user-examples repo have some warnings that didn't exist (or related to model options that didn't exist) when the models were created. In most cases, the models should be changed to make the warnings go away. This will make it easier to see when new warnings appear in the future. In a few cases, the warnings themselves may need revision in the SS3 code.

Warning files for these models aren't included in the model files like they are for the test models so a text file of each warning file is included below:
empirical_wtatage_and_age_selex
selex_age_example
selex_length_example
simple
simple_long
simple_long_wtatage
simple_with_discard

[Rick-Methot-NOAA]

In some cases the warnings were created because some models were not using good practices. So this current effort to reduce warnings is also accomplishing the goal of updating examples to use good practices.