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re: It turned out that many java limitations are very useful in long run. For example, quite strict linking between class and it's file name and locati...
 

I absolutely agree.

Though I am more focused on the conventions part that comes with Java, since that is probably the first thing a Newcomer encounters.

Most frameworks, especially in the EE Version are convention over configuration. Conventions are just that, they can be ignored.
Which you absolutely shouldn't, but hey, you could even use pointers and allocate memory yourself if you want, so theres that.

The conventions are, mostly, of intelligent design and as a bonus it saves you a lot of time you would otherwise spend on cumbersome configuration, by having sensible defaults.

CDI/JPA (especially compared to their initial/earlier versions) would be a great example of convention over configuration and how much is done in the background for you.

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