When I try to update to the latest version I receive the error message:
'Updating Software' has encountered a problem.
An error occurred while collecting items to be installed.
The Details message was;
An error occurred while collecting items to be installed
session context was:(profile=KNIMEProfile, phase=org.eclipse.equinox.internal.p2.engine.phases.Collect, operand=, action=).
No repository found containing: osgi.bundle,libphonenumber,6.3.0.0044727
Libphonenumber is required -as I know- only for the JSON nodes (JSON schema). Maybe as a workaround you can uninstall that feature and after a successful update install again?
Since my last message I was able to upgrade KNIME without problems (I also had JSON installed). The JSON extension is not just a node, but multiple. You are right that individual nodes cannot be uninstalled (except when the extension contains only one like the SAS7BDAT reader), only extensions/features.
Do you have a file named com.googlecode.libphonenumber_6.0.0.jar in your plugins folder? (It seems there might be a different extension causing this problem. The JSON dependency is com.googlecode.libphonenumber, not just libphonenumber... Do you have some special nodes installed which would use liphonenumber? Have you updated the json-schema OSGi bundle from an another source?)
In case nothing helps, you can install KNIME 2.12.1 to a separate folder, install the extensions you want to use and use it with the workspace you already have.
I am guessing, based on your Windows version that this is a quite new machine with more than 4GB RAM and so 64 bit version of Windows installed. Any 64 bit versions of them should be ok, though the last one is discoureged to unzip with the built-in zip handler as it might skip some files without warnings. If you do not want to install the extensions you need, you can safely use the KNIME + all free extensions for Windows (installer) too. If you prefer more compact installation and more control on what is extracted where, I would suggest one of the last two options.