LyX sometimes deletes a file and directory instead of making a pdf [No it doesn't]

[Boylan, Ross]

Follow-up on an issue from a few weeks ago:

On Fri, May 03, 2024 at 03:35:38AM +0000, I wrote:
> Since I'm not sure this is a bug, or what it's a bug in, I thought I'd post here.  First, I'd like to thank all the LyX developers for their work.
> 
> The core problem is that when I run `lyx -export pdf2 -v inst\doc\msep_num.lyx` under some conditions-detailed below---the .lyx file and the doc directory it is in are deleted, and no pdf is created in the top-level directory

To which Pavel replied, among other things,
>At the moment I don't see anything in the lyx code that would cause deletion of the file (or even the directory) itself.
>Unless it is some sideeffect of running of "git ls-files" which I strongly doubt...

which is true.  I tracked the problem down, and lyx was not the cause.  Some of the R packaging tools that were running lyx, were deleting the directory under some circumstances.

Thanks, Pavel, for your help.

Ross