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MSBUILD : error MSB4079: The <ProjectExtensions> element occurs more than once.
JTBuildInterface: Exception thrown while loading project: Microsoft.Build.BuildEngine.InvalidProjectFileException: The <ProjectExtensions> element occurs more than once.
at Microsoft.Build.BuildEngine.Shared.ProjectErrorUtilities.ThrowInvalidProject(String errorSubCategoryResourceName, XmlNode xmlNode, String resourceName, Object[] args)
at Microsoft.Build.BuildEngine.Shared.ProjectErrorUtilities.VerifyThrowInvalidProject(Boolean condition, XmlNode xmlNode, String resourceName)
at Microsoft.Build.BuildEngine.Project.ProcessProjectChildren(XmlElement projectElement, String projectDirectoryLocation, Boolean importedProject)
at Microsoft.Build.BuildEngine.Project.ProcessMainProjectElement()
at Microsoft.Build.BuildEngine.Project.RefreshProjectIfDirty()
at Microsoft.Build.BuildEngine.Project.InternalLoadFromXmlDocument(XmlDocument projectXml, ProjectLoadSettings projectLoadSettings)
at Microsoft.Build.BuildEngine.Project.LoadXml(String projectXml, ProjectLoadSettings projectLoadSettings)
at Microsoft.Build.BuildEngine.Project.LoadXml(String projectXml)
at JTBuildInterface.JTBuildImplementation.LoadAndInitProject(String ProjectFileName, String ProjectContent, ITaskHost TaskHost)
JTBuildInterface: Exception thrown while making file: Microsoft.Build.BuildEngine.InvalidProjectFileException: The <ProjectExtensions> element occurs more than once.
at Microsoft.Build.BuildEngine.Shared.ProjectErrorUtilities.ThrowInvalidProject(String errorSubCategoryResourceName, XmlNode xmlNode, String resourceName, Object[] args)
at Microsoft.Build.BuildEngine.Shared.ProjectErrorUtilities.VerifyThrowInvalidProject(Boolean condition, XmlNode xmlNode, String resourceName)
at Microsoft.Build.BuildEngine.Project.ProcessProjectChildren(XmlElement projectElement, String projectDirectoryLocation, Boolean importedProject)
at Microsoft.Build.BuildEngine.Project.ProcessMainProjectElement()
at Microsoft.Build.BuildEngine.Project.RefreshProjectIfDirty()

This error means that your project file (the .cbproj) contains more than one <ProjectExtensions> section. Open the project file in a text editor and remove the duplicate.

This is often caused by an upgrade from an older IDE version. The IDE ignores it, but the command-line compiler and TwineCompile require the project file to be correct.