Here's a tricky bug to track: The prune_downloads setting is not saved. As you mentioned in your wiki, this setting is important because the download table can grow very large and needs to be pruned. Here's how to reproduce this bug (testing in 2.2.9-post1):
Set the setting for prune_downloads in Links & Downloads > Hits and click 'Go' to save the setting. Click on any other LDM admin page (just to navigate away), and then click on the Hits page again. You'll see that the prune_downloads setting is reset to 0.
Partial work-around: You can set the prune_downloadtable in Links & Downloads > Settings > Hits Recording, and it will save your value. However, as soon as you navigate to the Hits page, the prune_downloads will reset to 0.
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