System crash on attempt to upgrade from 4.5.4 to 4.5.5

Hi!

This is my first bug report here.
Yesterday I installed 4.5.4 on fresh Drupal 7.
It was installed to 'sites/all/modules', but since there I keep library things, I had to move 'civicrm' module foder to 'sites/default/modules'.
Right after that I visited CiviCRM page from Navigation menu and was notified that new version is out, so I downloaded 4.5.5.
Then I started to read upgrade docs ( http://wiki.civicrm.org/confluence/display/CRMDOC/Upgrade+Drupal+Sites+to+4.5+-+Drupal+7 ) , and decided that the only thing I need is:
1) Disable CiviCRM modules except the main one - DONE. Actually there was only one module enabled except the main - CiviCRM theme. I disabled it.
2) Replace files from sites/default/civicrm with 4.5.5. DONE.
3) Clear cache. PROBLEM.

I'm using drush so I issued: drush cc all and got fatal error:
http://apaste.info/IOD

TL;DR:
require_once(CRM/Core/ClassLoader.php): failed to open stream: No such file or directory civicrm.settings.php:350
Error: require_once(): Failed opening required 'CRM/Core/ClassLoader.php'

I decided to skip this step, and proceeded to step 11 running the update script from browser: http://<your_drupal_home>/civicrm/upgrade?reset=1

I had been waiting for some time until the page loads but nothing happened and I went to sleep.

But when I woke up, mysql service was dead. I opened error log and discovered that it is ran out of diskspace. After I made some room and managed to run Mysql watchdog was about 10Gb!

Last records from the log:
http://apaste.info/OJH

TL;DR:
Warning: readdir() expects parameter 1 to be resource, boolean given in CRM_Utils_File::getFilesByExtension() (line 405 of /../sites/default/modules/civicrm/civicrm/CRM/Utils/File.php)

Honestly I thought installation wouldn't be such a pain.