Fix function reference in Shiny app; fix vignette build issues

[katy-sadowski]

• Fixes Warning: Error in convertJsonResultsFileCase: could not find function "convertJsonResultsFileCase" #459 by appending package name to convertJsonResultsFilecase call in Shiny app script
• Adds pdf rendering for new SqlOnly vignette to Packagemaintenance
• Fixes some configuration that was leading to issues running R CMD Check locally (pdfs in inst/doc were being deleted every time R CMD Check was run, but we want to keep these pdfs in the repo to comply with HADES documentation conventions)

[codecov]

Codecov Report

Merging #467 (7c65be2) into develop (f1a46fe) will decrease coverage by 0.48%.
The diff coverage is n/a.

❗ Current head 7c65be2 differs from pull request most recent head 17d8703. Consider uploading reports for the commit 17d8703 to get more accurate results

@@             Coverage Diff             @@
##           develop     #467      +/-   ##
===========================================
- Coverage    85.95%   85.47%   -0.48%     
===========================================
  Files           15       15              
  Lines          847      847              
===========================================
- Hits           728      724       -4     
- Misses         119      123       +4     

see 2 files with indirect coverage changes