Linux: Installation corrupt after updating old (1.6.x) installation

Existing installation:

• Installer creation time: 2015-01-20 - 12:34:03
• IFW Version: "1.5.82", Installer base SHA1: "7f2c98c", Build date: "Dec 8 2014".

1) Start ./MaintenanceTool
2) update qt.tools.maintenance from production (2.0.1)
3) click "Restart" button
4) Select Update components
5) Update qt.tools.qtcreator from production (3.4.0)
6) click "Finish"

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Side note, in console the following error message can be seen:

[142017] Warning: The current maintenance tool could not be updated. '/home/<user>/<path_to_installation>/.tempSDKMaintenanceTool' does not exist. Please fix the 'setInstallerBaseBinary(<temp_installer_base_binary_path>)' call in your script.

But despite this the maintenancetool version in the components.xml is 2.0.1 which is correct. And the maintenancetool itself has been updated correctly from 1.6 into 2.0.1 version as the login page has changed.
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Restart maintenancetool from command line using --addTempRepository <path_to_newer_qtcreator>

IFW Version: "2.0.1"
Build date: "May 12 2015"
Installer Framework SHA1: "af3555e"
[0] Language: en-US
[0] Arguments: ./MaintenanceTool, -v, --addTempRepository, <path_to_newer_qtcreator>
[324] Failure to read packages from: /home/iieklund/Qt/components.xml.
[324] Critical: Operations missing for installed packages ()
[324] Critical: Orphaned operations ("qt.tools.qtcreator", "qt.extras", "qt.extras.qtwebview", "qt.enterpriseaddons.qtpurchasing.src", "qt.extras.qtwebview.qt54.gcc_64", "qt.54.doc", "qt.53.gcc_64", "qt.extras.qtwebview.10.src", "qt.53.examples", "qt.enterpriseaddons.qtpurchasing.10.src", "qt.53.doc", "qt.enterpriseaddons.qtpurchasing.examples", "qt.extras.qtwebview.examples", "qt.54.qtwebengine.gcc_64", "qt.extras.qtcanvas3d.src", "qt.extras.qtcanvas3d.10.src", "qt.extras.qtwebview.doc", "qt.license.thirdparty", "qt.enterpriseaddons.qtpurchasing", "qt.extras.qtwebview.qt54.android_armv7", "qt.tools.maintenance", "qt.53.android_x86", "qt.license.enterprise", "qt.extras.qtcanvas3d", "qt.enterpriseaddons.qtpurchasing.qt53.gcc_64", "qt.cloudservices.enginio.10", "qt.enterpriseaddons.qtpurchasing.qt54.android_armv7", "qt.enterpriseaddons.qtpurchasing.doc", "qt.cloudservices.enginio.10.src", "qt.54.gcc_64", "qt.tools.maintenance.icons", "qt.54.android_armv7", "qt.53", "qt.54", "qt.enterpriseaddons", "qt", "qt.54.qtwebengine", "qt.54.examples", "qt.cloudservices", "qt.enterpriseaddons.qtpurchasing.qt53.android_x86", "qt.extras.qtwebview.src", "qt.tools", "qt.enterpriseaddons.qtpurchasing.qt54.gcc_64")
[324] created critical message box Corrupt_Installation_Error: 'Corrupt installation', Your installation seems to be corrupted. Please consider re-installing from scratch.