Update migrate app-config command to support migrate skipOn and timeout value in stage config

[khanhtc1202]

What this PR does:

Copy STAGE timeout and skipOn config under pipeline.stages[].with to pipeline.stages[] (Application config)

Why we need it:

We decided to make timeout and skipOn options available as stage config for all stages from pipedv1.

We keep the original timeout and skipOn config under pipeline.stages[].with for backward compatibility, in case users want to downgrade pipedv1 to pipedv0.
pipeline.stages[].with.{timeout, skipOn} will be marked as deprecated in v1.

Which issue(s) this PR fixes:

Part of #5542
Follow #6175

Does this PR introduce a user-facing change?:

• How are users affected by this change:
• Is this breaking change:
• How to migrate (if breaking change):

[codecov]

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 28.64%. Comparing base (e7ec5c4) to head (bbff1f1).
⚠️ Report is 2 commits behind head on master.

Additional details and impacted files

@@            Coverage Diff             @@
##           master    #6182      +/-   ##
==========================================
+ Coverage   28.43%   28.64%   +0.21%     
==========================================
  Files         537      537              
  Lines       57566    57579      +13     
==========================================
+ Hits        16367    16494     +127     
+ Misses      39927    39809     -118     
- Partials     1272     1276       +4     

Flag	Coverage Δ
.	23.28% <100.00%> (+0.26%)	⬆️
.-pkg-app-pipedv1-plugin-analysis	62.85% <ø> (ø)
.-pkg-app-pipedv1-plugin-kubernetes	60.24% <ø> (ø)
.-pkg-app-pipedv1-plugin-kubernetes_multicluster	67.48% <ø> (ø)
.-pkg-app-pipedv1-plugin-scriptrun	54.83% <ø> (ø)
.-pkg-app-pipedv1-plugin-terraform	38.31% <ø> (ø)
.-pkg-app-pipedv1-plugin-wait	35.51% <ø> (ø)
.-pkg-app-pipedv1-plugin-waitapproval	68.62% <ø> (ø)
.-pkg-plugin-sdk	50.37% <ø> (ø)
.-tool-actions-gh-release	19.23% <ø> (ø)
.-tool-actions-plan-preview	25.30% <ø> (ø)
.-tool-codegen-protoc-gen-auth	0.00% <ø> (ø)

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[ffjlabo]

👍

[Warashi]

🆗