@Unboggling - re timing of deletion. If I understand you properly your question concerns the situation where you dont clean the book straight away. A situation I have for much of my library given the earlier previous attempt to put it in my old library. What I do is a combination of things. Like Kacir mentioned, I have a #done custom column on each book to indicate I have cleaned/processed it. I also have an "Unprocessed" user category that I will add an author to if at the time I add a book I don't clean it right away (or they have so many books I just want to get them in and clean when I have more time). Strictly speaking the latter is kind of redundant since I could do a search for #done:false, but I like to see a count and list of the authors that are outstanding in my library, and a simple click on an author in that list in the tag browser gives me the books just for that author.
In terms of timing, as soon as I have processed (cleaned) a book any other formats in Calibre for it are deleted. As to when I delete from my source folders, I certainly do that when I have processed all books for that author, but sometimes for a specific book as I go. It depends on how I am processing the author, how many books they have and how many different versions of the book I have. Sometimes I end up doing a windows explorer search for a specific book rather than just the author, so I can more easily see and find my best format. In that situation it is just as easy to delete the files in the search results window when I have processed the book. That can help when you have an author who has short stories as well (which don't tend to be listed on Fantastic Fiction) and you are trying to figure out what books for that author you have not yet put in Calibre.
Note that a valid alternative that some people do instead of deleting is to move the books that they added into Calibre from their raw source folders into some other kind of "processed" folder. Just so they have them available should they do something bad with their conversions or find they picked the wrong format in thinking it was their best one. However I would certainly *not* attempt to store those in a Calibre library in any way - just use a filesystem search to find a book from there in the extremely rare circumstance you need to do so.
Re the 0.6 version - I'll be honest, I haven't read it in detail
. I saw spoilers within spoilers, and lots of text, and as I am not the target user for it anyway I moved on. I will say what I saw kind of read more as a "diary" than a quick summary?
If I was a user looking to get a quick and simple recommended setup, I don't really care about reading a whole paragraph or two of the "why" too much as a new user (if at all for many users I would suggest) - I just want to know the "what" to do and "when" to do it. The problem with explaining the why is that a why can be very verbose - after all, look at my own post here taking three paragraphs to explain some opinions on deletion.
I don't have the answers for you, as I saw someone else post writing documentation is freaking hard, and you have to do a fine balance between just enough to get them going without turning it into a whole user manual in its own right. Like I said, I am not your target user though, and others may find what you have done to be exactly what they were after so don't let me discourage you too much!