Also, I've been using ne for a decade now and want to thank everyone who's been involved in any way. A great little editor for those of us who do not love the arcane.
Thanks for the kind words, Ethan. I often wonder how many people use ne and how they feel about it, but we get very little feedback. Glad you like it.
As for files with "~" appended to their names... I'm not aware of a way ne would do that. Other editors do though, and some processes including "cp" and "rsync" will use a "~" suffix when given the --backup option. I'm pretty sure these files are the result of some process other than ne.
The only circumstances I know of where ne will save a file under a different name is when it's killed by an external signal. In that case, it would save any modified named buffers with a "#" prepended (as "#myfile.txt" for example), and modified unnamed buffers as "0x" followed by some hex characters. (I just tried it and got a file named "0x81f3400.1f41".)
In the first case, the files are saved in the same directory as the original file; in the second case, they are saved in whatever directory was current when ne was started. But the answer to your question is, no, there is no way to change the directory these files are saved into.