feat: refactor to use machinerun.io/atomfs

[rchamarthy]

What type of PR is this?

Refactor to use machinerun.io/atomfs as the atomfs library.

Will this break upgrades or downgrades?

No

Does this PR introduce any user-facing change?:

No

By submitting this pull request, I confirm that my contribution is made under the terms of the Apache 2.0 license.

[codecov]

Codecov Report

All modified and coverable lines are covered by tests ✅

Project coverage is 63.72%. Comparing base (a9a3809) to head (bdffc25).
Report is 1 commits behind head on main.

Additional details and impacted files

@@            Coverage Diff             @@
##             main     #640      +/-   ##
==========================================
+ Coverage   60.66%   63.72%   +3.06%     
==========================================
  Files          65       57       -8     
  Lines        6030     5015    -1015     
==========================================
- Hits         3658     3196     -462     
+ Misses       1618     1176     -442     
+ Partials      754      643     -111     

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