Update broken links in README.md

[e-perl-NOAA]

Updated broken links - these links look like they used to be in a repository called "ss-documentation" which is now called "doc" and the links have been updated accordingly.

Concisely (20 words or less) describe the issue

Please Link issue(s)

resolves #385

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

None, updating the readme links

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

Double check that links now work.

Has any new code been documented?

No need.

Check which is true. This PR requires:

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

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

If changes are needed in the change log, please fill in the table here:

Action	Topics	Type
[fix, new, or revise]	[e.g., biology. Use issue label options.]	[input, output, and/or calc, or ALL]

Additional information (optional):

[Rick-Methot-NOAA]

Thanks for working on this. The excel link should still go to "helper spreadsheets", not excel output viewer. The output viewer is an ancient precursor for r4ss.

[e-perl-NOAA]

@Rick-Methot-NOAA could you provide the link to that because I'm not seeing that anywhere in the repository - I might just be missing it somehow.

[e-perl-NOAA]

@Rick-Methot-NOAA The README.md now goes to the SS3 Shiny helper app and the phrasing in the readme has been changed accordingly.

[Rick-Methot-NOAA]

I looked over the whole readme and now think that it is better to refer to this shiny app within the list of tools rather than in this top section of the document.
Also, please add the link to the html version of the manual:
https://nmfs-stock-synthesis.github.io/doc/SS330_User_Manual.html

[Rick-Methot-NOAA]

looks good