Fix how virtual_packet properties are saved in hdf

[jaladh-singhal]

This PR makes sure that vpacket logging status is determined at run-time, thus removes any need of saving to a config file.

Description

• Removes all vpacket_logging.yml config file creation code implemented in log additional properties in hdf witeout when --with-vpacket-logging is present #967
• Uses runner.virt_logging to check if vpacket logging is enabled or not within hdf

Motivation and Context

Fixes #1246

How Has This Been Tested?

• Saved simulation to hdf file with vpacket-logging enabled, all vpacket_hdf_properties get saved.
• Saved simulation to hdf file with vpacket-logging disabled, none of the vpacket_hdf_properties get saved.

Screenshots (if appropriate):

Types of changes

• Bug fix (non-breaking change which fixes an issue)
• New feature (non-breaking change which adds functionality)
• Breaking change (fix or feature that would cause existing functionality to not work as expected)

Checklist:

• My code follows the code style of this project.
• My change requires a change to the documentation.
• I have updated the documentation accordingly.
• I have assigned/requested two reviewers for this pull request.

[codecov]

Codecov Report

Merging #1254 into master will decrease coverage by 0.02%.
The diff coverage is 66.66%.

@@            Coverage Diff             @@
##           master    #1254      +/-   ##
==========================================
- Coverage   80.63%   80.60%   -0.03%     
==========================================
  Files          41       41              
  Lines        3424     3419       -5     
==========================================
- Hits         2761     2756       -5     
  Misses        663      663              

Impacted Files	Coverage Δ
tardis/io/util.py	73.29% <50.00%> (-0.27%)	⬇️
tardis/montecarlo/base.py	87.50% <100.00%> (+0.07%)	⬆️

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