I wrote a wiki page about how to hack bootstrap --upload-tools so that it doesn't stop the controller from going through the normal processes of requesting tools from streams etc. This can be handy when that's the part of the code you want to debug, but you need to upload a custom binary with extra debugging information and/or changes to that code. It turns out that the changes are very minimal, they're just hard to find and spread out in a few different files.
Feel free to make corrections if there's anything I've missed or could do better: https://github.com/juju/juju/wiki/Hacking-upload-tools
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