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As of this version of the SDK, all files that are included as a module dependency in the manifest file must reside in the same directory as the manifest file when installed.  Other that that, you are free to install files however you wish.

Setting up the registry

Under the registry key HKLM\Software\Qbik Software\WinGate\Packages you need to create a key which has the same name as the package UUID in your manifest file. e.g. HKLM\Software\Qbik Software\WinGate\Packages\{F83CE035-1BA1-4B8A-BAB3-81FC56BD33D9}

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