Log queries:
------------

You could collect all the queries during core/plugin/theme upgrades to see what happens. Just follow these two steps:

1) You should add: 

    define( 'SAVEQUERIES', TRUE );

to your `wp-config.php` file to collect all queries during a page load into the `$wpdb->queries` array. Just remember to remove it afterwards.

2) Then you could log it into the `sql.log` file. Here's a simple example:

    /**
     * Dump all database queries to the /wp-content/sql.log file.
     */
    add_action( 'shutdown', function(){
    
        $file =  WP_CONTENT_DIR . '/sql.log';
    
    	if( current_user_can( 'manage_options' ) 
             && file_exists( $file )
             && is_writeable( $file )
             && isset( $GLOBALS['wpdb']->queries )
         )
             file_put_contents( 
                    $file, 
                    date( 'c' ) . PHP_EOL .  print_r( $GLOBALS['wpdb']->queries, TRUE ), 
                    FILE_APPEND 
             );
        
    });

Core upgrade files:
-------------------

For core upgrades these files might be of interest to you

   - /wp-includes/version.php
   - /wp-admin/includes/upgrade.php
   - /wp-admin/includes/schema.php

In the file `/wp-admin/includes/upgrade.php` you can find the upgrade function: `wp_upgrade()` that calls the `upgrade_all()` function. It contains database upgrades for each version in terms of functions like `upgrade_xxx()`

For example:

        ...truncated...

        if ( $wp_current_db_version < 22422 )
                upgrade_350();

        if ( $wp_current_db_version < 25824 )
                upgrade_370();

        if ( $wp_current_db_version < 26148 )
                upgrade_372();

        if ( $wp_current_db_version < 26691 )
                upgrade_380();

        maybe_disable_link_manager();

        maybe_disable_automattic_widgets();

        update_option( 'db_version', $wp_db_version );
        update_option( 'db_upgraded', true );


I hope this helps.