Java: How can I compile an entire directory structure of code ?

If all you want to do is run your main class (without compiling the .java files on which the main class doesn't depend), then you can do the following:

cd <root-package-directory>
javac <complete-path-to-main-class>

or

javac -cp <root-package-directory> <complete-path-to-main-class>

javac would automatically resolve all the dependencies and compile all the dependencies as well.

You have to know all the directories, or be able to use wildcard ..

javac dir1/*.java dir2/*.java dir3/dir4/*.java dir3/dir5/*.java dir6/*src/*.java

With Bash 4+, you can just enable globstar

shopt -s globstar

and then do

javac **/*.java