I love your question. I write my JavaScript very Object Oriented and keep my object constructors in their own files. I throw all of my .js files into a directory which I can organize into subdirectories any way I want. Then I run a "make" script. The following is a Bash script I wrote. I work at a Linux machine, so Bash scripting is a natural solution for me any anyone working in Linux.
#!/bin/bash
echo '' > temp0.js
find ./bin/external -name \*.js -exec cat {} >> temp0.js \;
echo ''> temp1.js
echo '(function(){' > temp1.js
find ./bin/prop -name \*.js -exec cat {} >> temp1.js \;
echo '})();' >> temp1.js
cat temp0.js temp1.js > script.js
rm temp1.js temp0.js
Forgive me if this bash scripting is amateurish. I'll readily admit in bash scripting I just hack together whatever works, but I like my JavaScript to be clean and organized and Object Oriented.
This bash script goes into a directory alongside a directory called "bin" which contains all the javascript .js files. In there, the subdirectory "external" contains various borrowed scripts like JQuery. I'm putting my own .js scripts in a folder called "prop" in the example above. The bash script gets all of these scripts and concatenates them. It also wraps my own prop files in an anonymous function to give them a private namespace (sortof).
I guess it's clear this isn't exactly what you wanted--Java--but I think this kind of option is what we have to make do with in JavaScript.