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I am experiencing an extremely serious issue: it seems that the javascript code in the Google Chrome extension is uncompressed.

I don't know but maybe compressing will have a performance boost. Considering content scripts are parsed and compiled each time a page loads, maybe it will have a good effect?

I have had good experiences with this: https://code.google.com/p/closure-compiler/

The entire extension is compressed: A CRX file is, at heart, a ZIP file.

It's okay for the Javascript itself to not be minified, because once the extension is installed, its own code doesn't need to be sent across the network, the main reason you'd minify in the first place; whitespace doesn't noticeably slow down the Javascript engine.