By definition, all Atari 2600/VCS emulators are cycle accurate.
That machine required very precise timing of the CPU to drive the video output.
There are a number of other cycle-accurate emulators, including some you woudln't expect, like a cycle-accurate emulator for the C64 floppy disk (needed for anti-piracy and some high-end demos that use the floppy like a co-processor).
rm ./~ is likely the easiest.
Another option, shell dependent, would be to turn off shell globbing.
The `GNU` version of `find` has a `-maxdepth` option so
find . -iname '~' -maxdepth 1 -exec rm {} \;
would work, but I don't like relying on `GNU` extensions.