fix: ensure run-id is added to resources in skaffold apply

[nkubala]

Fixes: #6657

Description
This change ensures that we add the skaffold.dev/run-id labels to all resources created in skaffold apply. This was not happening before this change, as the --add-skaffold-labels flag was not defined on the apply subcommand, causing the value to default to false.

The --add-skaffold-labels flag was deprecated in #5653 on May 5, 2021, putting us at just over 5 months since deprecation. Our deprecation policy would mandate a 6 month period, but I would propose an exception to this rule as this is the correct way to address this issue, and is a scenario that does not "fit neatly into this policy": https://skaffold.dev/docs/references/deprecation/#exceptions

As a result of this change, we will now always apply and skaffold-specific labels in Skaffold, with the exception of during skaffold render in which we will never apply them.

[gsquared94]

lgtm, with nit.

[codecov]

Codecov Report

Merging #6674 (fa32d85) into main (290280e) will decrease coverage by 0.70%.
The diff coverage is 35.29%.

@@            Coverage Diff             @@
##             main    #6674      +/-   ##
==========================================
- Coverage   70.48%   69.78%   -0.71%     
==========================================
  Files         515      523       +8     
  Lines       23150    23834     +684     
==========================================
+ Hits        16317    16632     +315     
- Misses       5776     6114     +338     
- Partials     1057     1088      +31     

Impacted Files	Coverage Δ
cmd/skaffold/app/cmd/flags.go	89.00% <0.00%> (-1.82%)	⬇️
cmd/skaffold/skaffold.go	0.00% <ø> (ø)
pkg/diag/recommender/container_errors.go	0.00% <0.00%> (ø)
pkg/diag/validator/pod.go	1.32% <0.00%> (ø)
pkg/skaffold/build/buildpacks/logger.go	0.00% <ø> (ø)
pkg/skaffold/build/cluster/logs.go	0.00% <ø> (-16.67%)	⬇️
cmd/skaffold/app/cmd/cmd.go	70.32% <66.66%> (-0.73%)	⬇️
pkg/diag/validator/resource.go	47.05% <66.66%> (ø)
cmd/skaffold/app/cmd/debug.go	100.00% <100.00%> (ø)
pkg/skaffold/build/buildpacks/lifecycle.go	83.59% <100.00%> (ø)
... and 82 more

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