More refactoring of internal DataPackageR() function, bug fixes

[slager]

Continue simplifying and factoring out smaller functions from the giant internal DataPackageR() function:

• validate_package_skeleton()
• validate_yml()
• get_yml_objects()
• get_yml_r_files()

Fix #128

• Simplify code in do_digests()
• Only run .compare_digests() once, assign result to object, then re-use (fixes the 3x part of Fix triplicate warnings when data version changes #128)
  • Messages and warnings were generated each time (3x) that .compare_digests() was run
• Don't throw a warning at all when objects change, just print info to console and logger (fixes the rest of Fix triplicate warnings when data version changes #128)
  • Warning didn't make sense because this is normal behavior when rebuilding a data package
• Adjust tests to reflect change

Misc fixes

• case-sensitive filename tweak in test should resolve warning thrown on Linux GitHub Actions runners
• Remove a logging file artifact that was accidentally committed in 2019

GitHub doesn't render the larger diffs very well due to some re-indenting

All tests still pass locally, and the only user-facing change is fixing the 3x warnings in #128.

[slager]

Looks like f0f6e93 did indeed solve the testthat warning on the Linux CI runners. The codecov runner also successfully uploaded results to their server, so either this fixed #122 also or the upload problem is intermittent.