convert natM(s to natM(t as first step in transitional SPR

[Rick-Methot-NOAA]

What issue(s) does this PR address? Describe and add issue numbers, if applicable.

#88 this conversion of natM indexing is first needed step

What tests have been done? Upload any model input files created for testing in a zip file, if possible.

runs with simple and hake_2018

What tests/review still need to be done? Who can do it, and by when is it needed (ideally)?

Check which is true. This PR requires:

• [x ] no further changes to r4ss
• [x ] no further changes to the manual
• [x ] no further changes to SSI (the SS3 GUI)
• [x ] no further changes to the stock synthesis change log (new features, bug reports)

Describe any changes in r4ss/SS3 manual/SSI/change log that are needed (if not checked):

Additional information (optional):

[Rick-Methot-NOAA]

@k-doering-NOAA please check to see that I did not disable your recent fix for fspr nan.
There are a lot of changes in this branch, so I want to get it merged in soon, but I also want to update the pred_M approach to be more fleet-like before I do. So look for that commit soon.

[k-doering-NOAA]

@Rick-Methot-NOAA I checked, and you did not disable the spr nan fixes. SO all good!

Let me know when you push your last commit, I can take a look at the code (or Neal could?) before it gets merged in!

[k-doering-NOAA]

Closing, because commits included in #307