[kpt deployer] Improve skaffold.yaml docs.

[yuwenma]

Related #3904

Description

• kpt.Dir is required, adding the explanation on the default config.
• kpt.applyDir is removed from top-tier config.
• Rewrote the kpt.Live struct to clarify the config scope and which configs should be considered together.
• Improve the kpt option docstring for skaffold users.

User facing changes (remove if N/A)

Changed the doc in skaffold.yaml for kpt deployer.

[yuwenma]

/cc @nkubala
/assign @MarlonGamez

[codecov]

Codecov Report

Merging #4799 into master will decrease coverage by 2.01%.
The diff coverage is 100.00%.

@@            Coverage Diff             @@
##           master    #4799      +/-   ##
==========================================
- Coverage   73.84%   71.82%   -2.02%     
==========================================
  Files         347      347              
  Lines       13798    11869    -1929     
==========================================
- Hits        10189     8525    -1664     
+ Misses       2973     2725     -248     
+ Partials      636      619      -17     

Impacted Files	Coverage Δ
pkg/skaffold/schema/latest/config.go	100.00% <ø> (ø)
pkg/skaffold/deploy/kpt.go	85.88% <100.00%> (-0.96%)	⬇️
pkg/skaffold/trigger/workdir.go	20.00% <0.00%> (-13.34%)	⬇️
pkg/skaffold/initializer/analyze/directory.go	50.00% <0.00%> (-10.00%)	⬇️
pkg/diag/validator/resource.go	50.00% <0.00%> (-8.83%)	⬇️
pkg/skaffold/logfile/logfile.go	71.42% <0.00%> (-8.58%)	⬇️
pkg/skaffold/runner/debugging.go	66.66% <0.00%> (-8.34%)	⬇️
pkg/skaffold/deploy/resource/status.go	77.77% <0.00%> (-7.94%)	⬇️
pkg/skaffold/runner/portforwarder.go	22.22% <0.00%> (-7.78%)	⬇️
pkg/skaffold/runner/render.go	12.50% <0.00%> (-7.50%)	⬇️
... and 339 more

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[MarlonGamez]

LGTM!