MySQL : Monitor Queries
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I am trying to understand a PHP - MySQL project. The Project is quite complex so exploring it line by line is quite impossible.

What I want to do is, compare the instances of a MySQL database.

Say,

1) MySQL is up and running. This is instance number one of the database.
2) A user logs in from PHP front end, and then logs out.
3) This is instance number two of the database.

I need to see what changed between instance one and instance two, in a friendly way. 

Any suggestions regarding open source tools or any other techniques?