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I've seen tinyBenchmarks slowdowns on the order of 3-5% from merely filing in change sets, regardless of what the change sets actually change. This was after loading about 200 updates for 2.9. At about 2990 there was a marked slowdown, but as it turned out, not related to a specific change set (and none of those around 2990+ contained any obvious potential speed-hogs in the code). I explicitly tried different sets with "harmless" changes and this gave a similar slowdown regardless. There was no obvious reason for this (like open change browsers).
This may result from loading a large number of updates (e.g. hundreds for 2.9a currently). Perhaps purging a lot of these update change sets (not the actual changes) will give you some speed back?
Henrik
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