Revise deployment stage timeout mechanism

[khanhtc1202]

What would you like to be added:

Every deployment should have its timeout to avoid long time blocking deployment. There is already pipeline.stages[x].timeout configuration (ref: https://github.com/pipe-cd/pipecd/blob/master/pkg/config/application.go#L225), but it is not to be used anywhere else.

Why is this needed:

[ffjlabo]

Ref: #4980

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