"I don't need to keep my java files in all those boring package name folders (e.g. /net/proj/...). I'll just keep them all in a single folder then let the compiler worry about it"
The above statement is true, but you should known that the IDEs like Eclipse, Netbeans, IntelliJ, assume that the java files are stored in folders according to the package structure.
The IDEs will report errors when you try to open the project in them. And sooner or later, you or someone on your team will want to do it.
The renaming process can be eased using the Eclipse refactor-move functionality, but it will be a pain, especially if your are using version control.
I wasted 2 days to rearrange the Java files to the standard structure using Eclipse and SVN.
You code, you learn!
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