fix: correctly rewrite /deploy/kubectl/manifests in patch upgrades

[mirober]

Fixes: #8564

Description
This looks like a fairly simple fix to me. #7800 added functionality to rewrite yaml paths in patches during v2->v3 upgrades. Only /deploy/kubectl/manifests should be rewritten to /manifests/rawYaml though, not all of /deploy/kubectl.

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[codecov]

Codecov Report

Merging #8585 (89756ff) into main (290280e) will decrease coverage by 6.24%.
The diff coverage is 54.32%.

@@            Coverage Diff             @@
##             main    #8585      +/-   ##
==========================================
- Coverage   70.48%   64.24%   -6.24%     
==========================================
  Files         515      610      +95     
  Lines       23150    30579    +7429     
==========================================
+ Hits        16317    19646    +3329     
- Misses       5776     9461    +3685     
- Partials     1057     1472     +415     

Impacted Files	Coverage Δ
cmd/skaffold/app/cmd/completion.go	13.04% <0.00%> (-1.25%)	⬇️
cmd/skaffold/app/cmd/config/list.go	65.21% <ø> (ø)
cmd/skaffold/app/cmd/config/set.go	88.72% <ø> (ø)
cmd/skaffold/app/cmd/config/util.go	54.28% <ø> (ø)
cmd/skaffold/app/cmd/credits.go	100.00% <ø> (ø)
cmd/skaffold/app/cmd/credits/export.go	0.00% <0.00%> (ø)
cmd/skaffold/app/cmd/deploy.go	40.90% <0.00%> (-12.94%)	⬇️
cmd/skaffold/app/cmd/generate_pipeline.go	60.00% <ø> (ø)
cmd/skaffold/app/cmd/inspect_modules.go	65.00% <ø> (ø)
cmd/skaffold/app/cmd/inspect_profiles.go	66.66% <ø> (ø)
... and 38 more

... and 388 files with indirect coverage changes

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