feat: Mark the VM as deleted

[yitsushi]

What this PR does / why we need it:

Mark the VM in the spec as deleted and let the reconciliation loop
handle it.

For mocking purpose, I introduced a Clock in ports.Collection.

Changed the event to Update event from Delete event. For the
reconciliation loop, they are the same. Let me know if we still want to
use the Delete event.

Which issue(s) this PR fixes:
Fixes #74

Special notes for your reviewer:
Changed the event to Update event from Delete event. For the reconciliation loop, they are the same. Let me know if we still want to use the Delete event.

Checklist:

• squashed commits
• includes documentation
• adds unit tests
• adds or updates e2e tests

Release note:

Mark the VM as deleted in the spec instead of deleting it on the Delete gRPC endpoint.

[codecov-commenter]

Codecov Report

Merging #124 (4f4329d) into main (ca14a16) will increase coverage by 0.30%.
The diff coverage is 83.33%.

❗ Current head 4f4329d differs from pull request most recent head dca8227. Consider uploading reports for the commit dca8227 to get more accurate results

@@            Coverage Diff             @@
##             main     #124      +/-   ##
==========================================
+ Coverage   40.09%   40.40%   +0.30%     
==========================================
  Files          32       32              
  Lines        1444     1448       +4     
==========================================
+ Hits          579      585       +6     
+ Misses        789      788       -1     
+ Partials       76       75       -1     

Impacted Files	Coverage Δ
core/application/commands.go	64.93% <83.33%> (+1.92%)	⬆️
pkg/queue/queue.go	100.00% <0.00%> (+6.06%)	⬆️

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