Rearrange config settings and global command line settings
The intention here is to have the config file content and parser be derivied from the command line types and flags. Now instead of having a saved config type that contains additional information to that kept in command line parameters we now put all the information in the command line settings type and make the saved config just the aggregation of the settings for various key commands like configure, install, upload. There's also an extended GlobalFlags type with the things like repos, cache dir etc. When we generate the initial config file we put in commented out versions of all (non-deprecated) valid fields, along with their default values. The aim is to make the config file self-documenting.
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