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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.