The package deployment overhaul is ending up being a much bigger job than I had anticipated. It has been worth it though so far.
Packages can now be uninstalled from a workstation successfully and then reinstalled, they no longer get lost in the ether.
Previously, the deployment used multiple SQL queries to handle something as simple as determining the list of packages available for install. Now, where possible, this has been condensed to just one query (including one with three joins).
Hopefully these changes will improvement the performance.
Kevin found one more bug for me so hopefully that will be the last of the package deployment overhaul.
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