Cannot upgrade site to 5.6.0.1 from 5.5.2.1

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I tried two different ways to upgrade concrete5 installation to 5.6.0.1 and both failed.

Method #1. Via normal "CONCRETE UPDATE" notification window.

Steps:
- click "Learn more and update"
- in the "Download update" window click "Download"
- in the "Install Local Update" window click "Update"
=> Upgrade to 5.6.0.1 complete!
- click Back to Home

Result:

Warning: include(/opt/www/www.mysite.com/updates/concrete5.6.0.1/concrete/themes/axe/layout.inc): failed to open stream: No such file or directory in /opt/www/www.mysite.com/updates/concrete5.6.0.1/concrete/core/libraries/view.php on line 418
Warning: include(): Failed opening '/opt/www/www.mysite.com/updates/concrete5.6.0.1/concrete/themes/axe/layout.inc' for inclusion (include_path='/opt/www/www.mysite.com/libraries/3rdparty:/opt/www/www.mysite.com/updates/concrete5.6.0.1/concrete/libraries/3rdparty:.:/usr/share/php:/opt/www/_common') in /opt/www/www.mysite.com/updates/concrete5.6.0.1/concrete/core/libraries/view.php on line 418

Question: why does concrete5 following successful upgrade want to load its core files from updates/ folder?

Method #2. Via instructions provided athttp://www.concrete5.org/documentation/how-tos/developers/manually-...

After upgrading, concrete5 is trying to load the custom theme called "axe" that we made before from concrete5/themes/ folder rather then from themes/ folder, where it resides... Re-installing/re-activating the theme doesn't help.

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Alas, neither method #1, nor method #2 work for us. Of course we tried to clear cache and even restart PHP-FPM and Memcached services.

Will appreciate feedback on the above issue.

Kind regards,

Andrejs

locojohn