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After updating to 10.8 ‘Mountain Lion’ I’m wondering how I can rebuild everything I have installed through the packaging system Homebrew (similar to MacPorts) to ensure all dependencies are installed optimally for the new system. How can it easily be achieved? The help file offers no hints as to how I can accomplish this.

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Use the command brew upgrade in the terminal to update all of the packages. As for rebuilding all of your programs for the new OS build, there is no reason to do this as the compiled binary should result as the same. If you are noticing any issues, I would just uninstall and reinstall the packages that you are having issues with.

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