In your Master page you would have something like this:
<head runat="server">
...
<asp:ContentPlaceHolder ID="htmlHead" runat="server" />
...
</head>
Then in your content page you would have something like this:
<asp:Content ID="Content1" ContentPlaceHolderID="htmlHead" runat="server">
<script type="text/javascript" src="js/custom.js"></script>
</asp:Content>
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