Believe me, Ken, I do not ask for help here before looking for a solution everywhere else: Google, FAQ, Docs,... in lots of places.
The point here is that .htaccess is recursive, and thus, you only have to put it in moodle main directory, but, as you suggested, php.ini is NOT recursive, and you have to put it in every directory you have to use, which I did not know and I find really anoying.
I created an upload script in PHP to check if .htacces and php.ini where working in my hosting provider: it worked fine with the file I was trying to upload, so the problem was only in Moodle.
After knowing the problem with php.ini, I copied it in the directories suggested in the Moodle Administration FAQ:
* root of your moodledata directory
But it still did not work. So, I made use of grep to find the file where the error appeared, and it was
So, I copied php.ini in the repository directory and a few others inside it, and Voila! It worked.
Now I am trying to find a way to make php.ini recursive, to have to put it only once in the moodle directory, but it does not work fine, and I get an error 500 (Internal Server Error). Any ideas on how to do that?