Tips for developers
An unsorted list of hints that you might find useful:
compile & execute a class
You do not need to call javac yourself with a long classpath:
$ ./fiji --javac YourClass.java
and you can call its main() method just as easy:
$ ./fiji YourClass.class argument1 argument2
rapidly prototype a plugin
It is often easier to start out with a Jython, JRuby or BeanShell script, as you do not have to care about strict typing, exceptions or recompiling. Just place your script (with the correct extension -- .py, .rb or .bsh) into the plugins/ folder and execute the script. Fiji will always execute the current version of the script, so you can edit and run the script without restarting Fiji.
Of course, it is even more convenient to use the Script Editor...
Once you have working code, you can turn it into a proper plugin (this is easiest with BeanShell, as its syntax is closest to Java already), adding strict typing and exception handling as needed.
find the .jar file containing a certain class
Sometimes, the compiler complains about a class not having a certain method or interface, but you know it must contain it. More often than not, that class exists in different versions in your classpath. Find out with
$ ./fiji bin/find-jar-for-class.py the.class.youre.looking.For