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Does anyone know of the practical reasons for the com.company.project package structure and why it has become the de-facto standard?
Does anyone actually store everything in a folder-structure that directly reflects this package structure? (this is coming from an Actionscript perspective, btw)
Preventing name-clashes is a rather practical reason for package structures like this. If you’re using real domain names that you own and everybody else uses their package names by the same role, clashes are highly unlikely.
Esp. in the Java world this is “expected behaviour”. It also kind of helps if you want to find documentation for a legacy library you’re using that no one can remember anymore where it was coming from 😉
Regarding storing files in such a package structure: In the Java world packages are effectively folders (or paths within a .jar file) so: Yes, quite a few people do store their files that way.
Another practical advantage of such a structure is, that you always know if some library was developed in-house or not.