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I have a project with a few org files that are exported as HTML to create a website. All org files that correspond to web pages have #+SETUPFILE: my-setup.org declared in it. And the my-setup.org file have all the common settings like the following.

#+language: en
#+html_doctype: html5
#+html_head: <link rel="stylesheet" type="text/css" href="css/stylesheet.css" />
......

Is there a way I can declare an HTML preamble content in the my-setup.org, so that it is applied to all the exported webpages.

I have already tried using the following solution from another question, and it doesn't work when added to my-setup.org.

# Local Variables:
# org-html-preamble: "My custom preamble!"
# End:

I don't want to add this preamble to my ~/.emacs.d/init.el file where I have the org-publish-project-alist configured, as this preamble should be part of the project repo.

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Try creating a file .dir-locals.el in the top-level directory of your project hierarchy and adding this content to it:

((org-mode . ((org-html-preamble . "My custom preamble!"))))

See Per-Directory Local Variables in the Emacs manual.

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