I should really think harder before I post. All I had to do was clear the cache. Problem was I couldn't from inside Joomla and I had to delete the cache folder.
I am using the Gemini template with Joomla 3.8.7 on a PHP 5.6 shared server.
I built the website in directory public_html/stage2/ while the old Joomla 1.5 website kept working at the top level.
Before launching the site at the top level I tested moving it to a different directory (public_html/staging/) to make sure that I didn't leave any absolute link with /stage2/ in the path. I then renamed /stage2/ to a different name so that any path with /stage2/ in it would be easeir to find.
When I did this test, I was surprised to find several instances of this /stage/ directory still appearing in what looks like the Gantry 5 framework.
1) The first and most apparent item is the logo of the site. The logo is stuck with this path:
src="/stage2/images/jls-inc-logo.jpg"
Even though in Gantry5 >> Base Outline >> Logo Particle the path is: gantry-media://jls-inc-logo.jpg
I simply cannot understand how this is possible. All the other images seem to have moved correctly, but not the logo.
For the record, this was a pretty easy fix since all I had to do was to enter /images/jls-inc-logo.jpg in the particle instead of gantry-media://jls-inc-logo.jpg and at least the logo part was fixed. The problem I see are the other two instances and the smattering of instances in the Database.
2) aside from the logo, /stage2/ also appears in the path of these two files below:
<script src="/stage2/templates/rt_gemini/js/juihelper.js"></script>
<script type="text/javascript" src="/stage2/templates/rt_gemini/js/headertabs.init.js"></script>
I spot checked the internal pages and in there only the logo seems to have /stage2/ in the path. It's likely that juihelper.js and headertabs.init.js are only called on the home page.
I searched for /stage2/ and stage2 (without the slashes) in the database and in the file system.
Inside templates/rt_gemini there is no trace of either strings.
3) In the database I found /stage2/ in the following tables:
Incidentally, this is the first time I see this happen with Joomla where the error wasn't mine (or, more precisel, where I didn't write the path myself and forgot about it.
It could still be my error, but for the life of me I can't figure out where I messed up.
Thank you for your help.