You don't say much about your level of Moodle experience. I hope I avoid either patronising you, or going way over your head.
I assume you have gathered (from the upgrade docs, if nowhere else) that a Moodle site comprises three bits:
- The code (often in a folder called moodle - this folder is where the config.php file, which contains the database name and password, lives.)
- The uploaded files (often in a folder called moodledata)
- The Moodle database.
A really good idea is if you can copy all of that onto some other computer, where you can safely experiment on the copy, before you do something bad to your real site. See Moodle migration.
OK, so really what you want to do is work out exatly which version of Moodle you have installed. That information should be on the admin notifications screen. Alternatively, (if your site is not too old) the may be a file called githash.php in the same folder as the config.php.
Then, you can download a clean copy of exactly that version of Moodle. If you go to , you will see that the link to download the latest version from teh 1.9 branch is http://download.moodle.org/download.php/stable19/moodle-1.9.19.zip. Suppose you find you are actually using Moodel 1.9.3, then if you guess what the download URL is, you will be right
Then, using a tool like diff, or Winmerge, you can compare that clean download with what you have got.
All Moodle plugins live in a single folder. For example, if you find a folder in your version, but not in the standard version, called mod/certificate, then that means your site has the certificate module installed.
If you are familiar with the version control system git, then you can use that to do the file comparison in a more sophisticated way.