Best practices for package directory structure?

Question

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?

Answer 1

hmm, there's a lot to absorb here...
I found these articles online that seem good:
http://www.onjava.com/pub/a/onjava/2003/12/17/ant_bestpractices.html
http://www.kevinboone.com/classpath.html
I'd like to use ant if possible & understand it; I've had troubles with IDEs in the past and would like to just stick with basic build mechanisms.
I guess as a practical example let's say I have two different applications that use the serial port, that I want to release separately, each in separate .jar files. One is called com.example.applications.serial1 and the other is com.example.applications.serial2. They both use rxtx.org's gnu.io.* libraries. Serial1 uses some packages that I have developed: com.example.tools.spinner and com.example.tools.flapper, whereas Serial2 uses com.example.tools.spinner and com.example.tools.flopper
I think I want to organize things this way: (everything below under /java/src/)
com
example
applications
serial1
serial1.java
serial2
serial2.java
tools
spinner
spinner.java
flapper
flapper.java
flopper
flopper.java
and I think I want to compile to /java/classes/:
com
example
applications
serial1
serial1.class
serial2
serial2.class
tools
spinner
spinner.class
flapper
flapper.class
flopper
flopper.class
but I'm sort of lost on where to put the ant buildfiles, which directories to be in to run javac, and how to get the jar files right. From what I've searched for online, the external libraries (RXTX's jar files & .dlls for windows) are "interesting", and the easiest thing is to tell users of my .jar files to put the rxtx libs in the same library as the .jar files so I can set the Class-Path: in the .jar manifest to point to them.