Version 1.1.0 of Package Control was just released for upgrade. Changes include:
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Support for local Git and Hg repositories in addition to zip/.sublime-package downloads
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Fixed Discover Packages command to pull the proper URL from custom repositories
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Improved the handling of upgrades and removal on Windows, reducing the number of Access Denied errors
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Changed the downloaders to try multiple times on timeout since GitHub and BitBucket requests seem to fail fairly frequently
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Package upgrades now copy the complete old version to the Backups folder that is a sibling of the Packages directory
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Fixed the text of the activity indicator during individual package upgrades
Also, the master channel list has been updated to include github.com/Kronuz/SublimeLint.
Thanks for all of the feedback and suggestions, keep them coming!
I very much apologize for causing you to lose work with Upgrade All Packages. This new version should prevent such loss, and should also make it possible for less network-intensive updates via git and hg.