Add multiple new checks

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ADDED - check for /var/cpanel/mysql_upgrade_in_progress, as this may break the MySQL Upgrade UI:

[WARN] * /var/cpanel/mysql_upgrade_in_progress: exists! See case 113349.

Requested by:
  Eric Delorme

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UPDATED - /var/cpanel/users file ownership check now ignores the "cp12345678abcdef"-format temporary users added by the ticket system.  While I was here, prevented "readdir/closedir() attempted on invalid filehandle" errors if /var/cpanel/users directory is missing (however unlikely that is) in this check and one other related check.

Requested by:
  Peter Elsner

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ADDED - Check if "root" in cpanel.config is changed from the default.  This will break WHM if it is invalid:

[WARN] * /var/cpanel/cpanel.config: root set to "/usr/"
         \_ Default is "/usr/local/cpanel"
         \_ An invalid root setting can cause WHM to fail to start.  See ticket 5463121.

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ADDED - Check for additional MySQL configuration files that can be parsed by mysqld.  Some of these are listed in "mysqld --help", some were only found by looking at /usr/bin/mysqld_safe code, and strace data.  I've confirmed they all work and can therefore break MySQL.  A real-world example of this is in ticket 5443509.

[WARN] * MySQL - extra my.cnf files found: [ /etc/mysql/my.cnf /usr/my.cnf /usr/etc/my.cnf /var/lib/mysql/my.cnf ]
         \_ These may replace or be merged with /etc/my.cnf settings!

Requested by:
  Sean Malen

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