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So.what do you suggest? Deliver an upgrade script?
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Well we could make it atomic if we make the upgrade gluon only. gluon could be a symlink or a junction point in windows, so all upgrade would do would be to download gluon_2_9_12 unzip it and change the gluon symlink to point to gluon_2_9_12 instead of pointing to gluon_2_9_11.It will obviously never be possible to upgrade automatically if the process doesn't have permissions to do it, but the same could be said for code editing in admin and we still have that feature. This could be checked before performing the upgrade.