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I try to setup a basic, easy website workflow. Right now I can simply press C-e P x project-name, export and upload my Org, image, and whatnot files as HTML. As I don't want to upload that directly into /var/www, because you'd need special permissions, I want to run a command right after publishing on my webserver.

Is there a more elegant (better: more robust) way of solving the issue, besides running some kind of command/script after org-publish?

I tried to do that via inotify/a random inotify script I found on SO, but it won't recognize the changes I made, poor inotify script. :(

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You can look here. I'm pretty sure the Apache log example is close to what you want. So this would be something like:

#!/bin/sh
while inotifywait -e modify <your-export-directory>; do
  # do something...
  cp -r <your-export-directory> /var/www
  # ...or other
done

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