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To make a new version of the flow msi you need two Guids. One for the product (upgradecode) and one for the folder in the start menu.
Create your GUIDS here: http://www.guidgenerator.com/online-guid-generator.aspx^{Image Removed}

1 Change the msi name OutputName tag in the properties of the wix project (WaterFlowModel1D.wixProj)wixProj file. Keep the suffix of buildnumber as it adds a buildnumber to the msi name.

Changes in the Product.wxs:
2 Change the <?define ProductVersionReleaseVersion="1.0.1.xxx" ?> element and <ProductName> in the Product.wxs
3 Change the GUID for the UpgradeCode in the <Product> element.
4 Use the same GUID as in 3 for the <Upgrade> elementID
5 Change the GUID of the ProgramMenuDir" component.Like this <Component Id="ProgramMenuDir" Guid="CHANGE-THIS-GUID">

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