New to Java

I've only compiled a few java programs & while I find the language itself very easy to adapt to from C++ and Javascript, I get confused about the directory structure and classpaths & such.

My main method of operation is to build small tools and test projects, and I would like to follow good practices for organizing my directory structure, so it will (a) work well with java, and (b) work well with my source control software.

Let's say I am developing packages named "com.example.test.test1", "com.example.test.test2", "com.example.tools.flapper", and "com.example.tools.spinner".

I know I can use this structure:
/java/test/test1/com/example/test/test1/* (files for com.example.test.test1 including test1.java)
/java/test/test2/com/example/test/test2/* (files for com.example.test.test2 including test2.java)
/java/tools/flapper/com/example/tools/flapper/* (files for com.example.tools.flapper including flapper.java)
/java/tools/spinner/com/example/tools/spinner/* (files for com.example.tools.spinner including spinner.java)

But the directories seem unnecessarily deep & lead to a hassle in source control that makes it difficult to browse.

Can I use this? and if so, how do I run "javac" and "jar" properly to compile/jar-ify each package?
/java/com/example/test/test1/* (files for com.example.test.test1)
/java/com/example/test/test2/* (files for com.example.test.test2)
/java/com/example/tools/flapper/* (files for com.example.tools.flapper)
/java/com/example/tools/spinner/* (files for com.example.tools.spinner)

also is it recommended to leave the .class files in the same dirs as the .java files, or better to have a separate tree for compiled .class files?