Create README files at assay folder level, and clean up inst/ folder

[kelliemac]

Description

Instead of creating a README file for each PT report at the time of knitting to visc_pdf_document or visc_word_document, the README file will now be at the assay level and created at the first time that use_visc_report() is called within an assay folder.

Related Issues

Related to #92

Checklist

• This PR includes unit tests
• This PR establishes a new function or updates parameters in an existing function
  • The roxygen skeleton for this function has been updated using devtools::document
• I have updated NEWS.md to describe the proposed changes

[kelliemac]

@mayerbry to review this PR! Alicia gave verbal approval at our meeting today.

[kelliemac]

Per group discussion on 1/7, ok to move templated README to assay level, and also create a blank README file for each report.

[codecov]

Codecov Report

Attention: Patch coverage is 96.66667% with 1 line in your changes missing coverage. Please review.

Project coverage is 82.50%. Comparing base (b8969f4) to head (3be81bf).

Files with missing lines	Patch %	Lines
R/visc_output_document.R	85.71%	1 Missing ⚠️

Additional details and impacted files

@@             Coverage Diff             @@
##           develop     #233      +/-   ##
===========================================
+ Coverage    82.10%   82.50%   +0.39%     
===========================================
  Files            8        8              
  Lines          352      360       +8     
===========================================
+ Hits           289      297       +8     
  Misses          63       63              

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[kelliemac]

since I moved around some of the relevant files, I will go ahead and address #241 now too

[kelliemac]

I also added a note about using git tags instead of hashes, in line with #238

[kelliemac]

@mayerbry and @slager can you please review this PR when you have a chance? I increased the scope a little bit because I got frustrated with the organization of files in the inst folder while I was updating the README creation steps. so I renamed a bunch of files (all within inst) but didn't actually change their contents for the most part. we had discussed in the past that it was sometimes difficult to find the right files to edit in this package, so I'm hoping the new organization helps with that.

please focus on the following in your review:

• are the new file names and organization of the inst folder more intuitive than before? are these changes + the additional text in the package README sufficient to address Add quick links in package README for important files #241?
• are the updated README formats of inst/templates/README_assay_folder.md and inst/templates/README_report_folder.md acceptable?
• do you have any concerns about the code changes in use_visc_report.R and visc_output_document.R?

thank you!!!