Hi Ceyhun,
Just to clarify one more thing about the temporary application instance WebIDE creates for your. It gets created so a single developer can test its work on WebIDE independently from other developers on the same org/space. Once you stop the app via WebIDE it deletes the instance from your org/space.
Whenever you build the whole MTA project it generates an mtar file which you can deploy to your org/space. The difference here is that this mtar files will deploy all modules in a single run. In that sense, if you chose to deploy the mtar files in addition to running the NodeJS module, you will probably end up with two instances of the same software taking up valuable resources such as routes and memory.
In addition to this the mtar file will probably represent a candidate to become productive software. And if your have dev/ops in place with continuous integration software it can pickup the mtar file to deploy automatically via CF CLI on another org/space (probably a test space) and later on a productive org/space. You could also investigate the blue/green deployment for such use cases.
Regarding the IDE I think there is no correct way to go or even best practices. Some will say that serious native cloud development has to be done with Eclipse or IntelliJ IDEA, whereas other may say VS-Code is the way to go and there are people such as yourself that may prefer a web tool. I strongly believe that all tools are valuable assets in some specific areas whereas others are stronger with something else.
What I can say about WebIDE is that you ought to probably work heavily with Git and CI/CD tools. For that you can read the following document which deals with thoroughly.
Best regards,
Ivan
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