Thanks to @NickD’s successful attempt to compile, I was able to identify the issue.

It lies in the :base-directory and the :exclude variables. The latter variable inherits from the former.

In details:

;; Define the publishing project
(setq org-publish-project-alist
      '(
        ("notes"
         :base-directory "./.."
         :base-extension "org"
         :publishing-directory "./public"
         :exclude "./")

I thought that the :exclude variable would take the same base value as the :base-directory one. In other words, let’s say I have .site where I execute my commands and my based directory is a folder up, I set :base-directory to ./... I also set the :exclude variable to ./ to exclude the directory I am executing the script in, here .site. However, :exclude inherits from :base-directory, therefore actually excluding my base-directory to be published….

To solve the issue, all I need to refer the exclude directory from the :base-directory starting point. So this works:

(setq org-publish-project-alist
      '(
        ("notes"
         :base-directory "./.."
         :base-extension "org"
         :publishing-directory "./public"
         :exclude ".site/")

[EDIT]

Nope, I’m wrong. What’s written below is incorrect. Refer to the comments below this answer for the correct answer.

Thanks to @NickD’s successful attempt to compile, I was able to identify the issue.

It lies in the :base-directory and the :exclude variables. The latter variable inherits from the former.

In details:

;; Define the publishing project
(setq org-publish-project-alist
      '(
        ("notes"
         :base-directory "./.."
         :base-extension "org"
         :publishing-directory "./public"
         :exclude "./")

I thought that the :exclude variable would take the same base value as the :base-directory one. In other words, let’s say I have .site where I execute my commands and my based directory is a folder up, I set :base-directory to ./... I also set the :exclude variable to ./ to exclude the directory I am executing the script in, here .site. However, :exclude inherits from :base-directory, therefore actually excluding my base-directory to be published….

To solve the issue, all I need to refer the exclude directory from the :base-directory starting point. So this works:

(setq org-publish-project-alist
      '(
        ("notes"
         :base-directory "./.."
         :base-extension "org"
         :publishing-directory "./public"
         :exclude ".site/")