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We have an internal application where writing MBTiles is the performance bottleneck, making these changes gave us some meaningful improvements.
Instead of having each Encode method return a new list (or yielding results) and then adding them to the Geometry using AddRange, pass in the Geometry list and add the contents directly.
This gives us a ~12% performance increase in our internal testing.
If id is a ulong, set it directly instead of ToString and Parse it. Another small performance improvement.