Since there is no Bug forum I am going to post this here.

I had this function in file named reserv.php that was being called from 'includes/functions.php'
The function name was date_diff().
When I right clicked on it and selected 'Find Declaration' I was not sent to the functions.php in the includes folder.
I was sent to 'site/includes/functions.php' (a backup I have of the site inside the site)

So what is the 'Find declaration' doing? I think it's looking at every file in the project for the declaration of the date_diff function, which is completely wrong (as you can see in this scenario).
It should analyze the current file and look for require or include or something like that, something that would prevent it from giving me the wrong file.

This gave me quite a headache, because I then upload the file to the server and no changes took effect because I was editing the wrong file.

Hope this can be corrected!!!

Seems you need to read php manual and check how it works in more details.
In short, it's not necessary to have any include/require statements in your file and get all the functions either from "site/include/functions.php" or "include/functions.php" to be accessible.
Just a trivial example:
fileA includes "site/include/functions.php" and also includes your file where you call date_diff().
In this case date_diff will be called in site/include/functions.php.
fileB includes "include/functions.php" and also includes your file where you call date_diff().
In this case date_diff will be called in include/functions.php.

I'd recommend you to remove backup (and all other possible duplications) from the project tree. You can do this by adding its directory name into the "Hide directories" in the project properties or placing the directory into another project or at least out of current project.

Please do not think to teach me php.

I know very well functions are global, but if there is an include file in the current file phped should check if that file includes the function so I don't go back and forth for almost an hour checking why the code didn't update

IDE can not distiguish if include "include/functions.php" actually includes "site/include/functions.php" or "include/functions.php".
For example you might have "site" directory in your include_path setting in php.ini and therefore include would find "site/include/functions.php".