refactor: Remove archived/outdated workflows and scripts

[ivadym]

This PR:

Having dead code in the project that keeps popping out when I do global searches is annoying. I'm removing it.

Removed:

• Archived/outdated workflows and scripts

Review and tests:

• Tests pass
• Code review
• New code is executed and covered by tests, and test approve

[sonarcloud]

Kudos, SonarCloud Quality Gate passed!   

0 Bugs
0 Vulnerabilities
0 Security Hotspots
0 Code Smells

No Coverage information
No Duplication information

[codecov]

Codecov Report

All modified and coverable lines are covered by tests ✅

Files	Coverage Δ
BALSAMIC/commands/base.py	100.00% <100.00%> (ø)
BALSAMIC/commands/config/base.py	100.00% <100.00%> (ø)
BALSAMIC/commands/config/case.py	100.00% <100.00%> (+3.44%)	⬆️
BALSAMIC/commands/config/pon.py	100.00% <100.00%> (+4.87%)	⬆️
BALSAMIC/commands/init/base.py	100.00% <100.00%> (ø)
BALSAMIC/commands/options.py	100.00% <100.00%> (ø)
BALSAMIC/commands/report/base.py	100.00% <100.00%> (ø)
BALSAMIC/commands/report/deliver.py	100.00% <100.00%> (ø)
BALSAMIC/commands/report/status.py	100.00% <100.00%> (ø)
BALSAMIC/commands/run/analysis.py	100.00% <100.00%> (ø)
... and 18 more

📢 Thoughts on this report? Let us know!.

[mathiasbio]

Those scripts look like they could be useful, or have been useful at some point. But we can dig them out of the grave in the future (💀 🧙 💚 ) if we realise we need to make coverage-plots from sambamba, or plot mutational signatures, or want to...I don't know exactly what VariantReport was used for...filtering variants and calculating TMB? 🔥