So clone first downloading all patches and do required steps and fails in renaming from tempopary dir.

Should be in reverse order, right? :)

$ pijul clone https://nest.pijul.com/pijul/pijul
✓ Updating remote changelist
✓ Applying changes      196/196
✓ Downloading changes   196/196
✓ Outputting repository
Error while renaming "/home/mpech/.tmp0hJlI7" to "/home/mpech/pijul": Directory not empty (os error 39)

I just fixed this. One issue was to clean things up if anything fails, or clone is interrupted.

Good