Moves check_input_data to SystemTestsCommon when running a test

[jasonb5]

When running a test, check_all_input_data is called from run_indv
of SystemTestsCommon rather than case.submit. This will solve
issues when the second or nth case of a test needs additional data.
If the test cannot download the data, the user is presented an error
suggesting to run ./check_input_data manually from within the
caseroot.

Test suite: pytest tests
Test baseline: n/a
Test namelist changes: n/a
Test status: n/a

Fixes #4400
User interface changes?: N
Update gh-pages html (Y/N)?: N