Some hot fixes/features for Vulcan

[amadeovezz]

BUG FIXES

• Use config values as params instead of named snakemake params
• Comment out flakey tests (until race condition is fixed on CI)

NEW FEATURES

• Modify what files are returned when downstream files are stale

[graft]

Don't forget to disable health_check at lib/ssh_connection_pool.rb:36, I did not do this on my latency branch.

[amadeovezz]

the work in this PR has transferred to:

• Other fixes: Vulcan fixes #1440
• Downstream files: Improved state management #1447