[Improvement]: Improve the consistency in bal run and bal build behavior

[azinneera]

Description

Currently, the bal run does not generate the executable which is not consistent with the behavior in bal build + java -jar execution flow. This resulted in unexpected behaviors for manual tests (e.g https://github.com/ballerina-platform/ballerina-lang/issues/40253 is not reproducible with bal run). Also, LifeCycle compiler plugins are not executed in bal run since it is executed only after the executable is generated.

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Related area

-> Compilation

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