fix: sync slow

[ericzzzzzzz]

Fixes: #8166

#8249 fixed #8166, #9029 accidentally removed skipDir logic which caused the regression, this pr added corresponding logic back.
Test plan is in #8249

[codecov]

Codecov Report

Merging #9167 (0ec203e) into main (290280e) will decrease coverage by 6.76%.
Report is 1064 commits behind head on main.
The diff coverage is 48.51%.

@@            Coverage Diff             @@
##             main    #9167      +/-   ##
==========================================
- Coverage   70.48%   63.72%   -6.76%     
==========================================
  Files         515      630     +115     
  Lines       23150    32447    +9297     
==========================================
+ Hits        16317    20678    +4361     
- Misses       5776    10183    +4407     
- Partials     1057     1586     +529     

Files	Coverage Δ
cmd/skaffold/app/cmd/commands.go	97.61% <100.00%> (+0.35%)	⬆️
cmd/skaffold/app/cmd/config.go	100.00% <100.00%> (ø)
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/debug.go	100.00% <100.00%> (ø)
cmd/skaffold/app/cmd/flags.go	93.00% <100.00%> (+2.18%)	⬆️
cmd/skaffold/app/cmd/generate_pipeline.go	60.00% <ø> (ø)
cmd/skaffold/app/cmd/init.go	100.00% <100.00%> (ø)
... and 41 more

... and 433 files with indirect coverage changes

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