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The first book was done as part of a writing class. He had an outline of the entire series at that time, originally planned as 20 "casefile" books followed by a trilogy to cover the Apocalypse. Last I recall he said he was a book or two behind that original count. I dont know anyone that has actually seen said outline though, so I couldnt comment on what details appear in it.
There are certain things that are known to have changed and/or evolved since that original plan. Both Ivy and Butters were originally more or less through-away characters that became useful later, for example. Also the events of Proven Guilt were originally planned before Dead Beat, but was re-arranged once it was confirmed that Book 7 was to be the first in Hardback (wanted a less intimate, more action-packed story that could be a decent entry point for new readers).