All JS compresses do is remove all the white space - it's all they can do. In the long run, if you're creating large Javascript files then Prototype will be able to shave a lot off of the file sizes due to the short-handed ways of writing the code. Such as $() instead of document.getElementById().

If you want to be your own Javascript compressor then once you're done, please all your Javascript on one huge line - of course keep another version that is formatted in a drop dead gorgeous way so that you can easily edit it. The good thing about Javascript is that it doesn't need the semi-colons at the end of each line, unlike PHP, and so removing those for each line will save you countless bytes!

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The man who comes back through the Door in the Wall will never be quite the same as the man who went out.