The first biggest problem was that Drupal was displaying Access denied message on all web pages. It was not possible to login to system. Even http://localhost/?q=admin didn’t work.
I had to create temporary session. It is quite easy when using Drush:
Drush displayed one time session for admin. This solved the problem with admin login.
The other issue was that there was Access denied message on every page. There were also other very useful messages flooding each page:
Notice: Undefined index: access in function _menu_link_translate() …
I spent some time searching for any hint how to resolve this weird behavior. It was necessary to delete all Drupal’s caches.
Configuration -> Development -> Performance -> Delete cache
After this clean up Drupal was working correctly.
Then I checked one older Drupal 6 site and there was nice big red warning:
Warning: strtotime() [function.strtotime]: It is not safe to rely on the system’s timezone settings. You are *required* to use the date.timezone setting or the date_default_timezone_set() function. In case you used any of those methods and you are still getting this warning, you most likely misspelled the timezone identifier.
The problem was that there was no default timezone in php.ini. It was sufficient to add timezone to /etc/php5/apache2/php.ini to section
[Date] ; Defines the default timezone used by the date functions ; http://php.net/date.timezone date.timezone = "Europe/Prague"
You can find more info about timezones at php.net/date.timezone.
After reloading Apache configuration everything was ok.