This issue is that my linked CSS and JavaScript files are loading below the <body> tag, rather than being in the head.
Should I be doing something like this?
<!--SPM:<SharePoint:CssRegistration runat="server" Name="/sites/test/Style Library/custom.css" After="SharepointCssFile" />-->
<!--SPM:<SharePoint:ScriptLink language="javascript" name="custom.js" OnDemand="true" runat="server" Localizable="false"/>-->