MobaXterm uses "%USERPROFILE%\Documents" as work folder unless Documents have been redirected to a network share. In that case it will default to %APPDATA% instead. This template is based on the %APPDATA% location.
You can now find this template in my GIThub repository
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<?xml version="1.0"?>
<SettingsLocationTemplate xmlns="http://schemas.microsoft.com/UserExperienceVirtualization/2013A/SettingsLocationTemplate">
<Name>Mobatek MobaXterm</Name>
<ID>Mobatek-MobaXterm</ID>
<Version>1</Version>
<Author>
<Name>Djerf</Name>
<Email />
</Author>
<Processes>
<Process>
<Filename>MobaXterm.exe</Filename>
</Process>
</Processes>
<Settings>
<Registry>
<Path Recursive="true">SOFTWARE\SimonTatham\PuTTY</Path>
</Registry>
<Registry>
<Path Recursive="true">SOFTWARE\Mobatek\MobaXterm</Path>
</Registry>
<File>
<Root>
<EnvironmentVariable>APPDATA</EnvironmentVariable>
</Root>
<Path>MobaXterm</Path>
<FileMask>MobaXterm.ini</FileMask>
</File>
<File>
<Root>
<EnvironmentVariable>APPDATA</EnvironmentVariable>
</Root>
<Path>MobaXterm</Path>
<FileMask>MobaXterm backup.zip</FileMask>
</File>
<File>
<Root>
<EnvironmentVariable>APPDATA</EnvironmentVariable>
</Root>
<Path Recursive="true">MobaXterm\slash\etc</Path>
</File>
<File>
<Root>
<EnvironmentVariable>APPDATA</EnvironmentVariable>
</Root>
<Path Recursive="true">MobaXterm\slash\var\log</Path>
</File>
<File>
<Root>
<EnvironmentVariable>APPDATA</EnvironmentVariable>
</Root>
<Path Recursive="true">MobaXterm\slash\usr</Path>
</File>
<File>
<Root>
<EnvironmentVariable>APPDATA</EnvironmentVariable>
</Root>
<Path Recursive="true">MobaXterm\home</Path>
</File>
</Settings>
</SettingsLocationTemplate>
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