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Windows Tray Notifier
You will need to upgrade windows tray notifier by uninstalling it and installing it again. Unfortunately, auto-upgrade will not work due to issues in old version of Windows Tray Notifier.

Maven runner
In earlier TeamCity versions Maven was executed by invoking the 'mvn' shell script. You could specify some parameters in MAVEN_OPTS and some in UI. Maven build runner created its own MAVEN_OPT by concatenating these two (%MAVEN_OPTS%+jvmArgs). In this case, if some parameter was specified twice - in MAVEN_OPTS and in UI, only the one specified in MAVEN_OPTS was effective.

Starting with TeamCity 6.5 Maven runner forms direct java command. While this approach solves many different problems, it also means that MAVEN_OPTS isn't effective anymore and all JVM command line parameters should be specified in build runner settings instead of MAVEN_OPTS.

Open API Changes
Several return types have changes in TeamCity open API, so plugins might need recompilation against new TeamCity version to continue working.
Also, some API was deprecated and will be discontinued in later releases. It is recommended to update plugins not to use deprecated API.

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