Hey Leo, are you trying to use Ext 3 or 4 to define the new class? If Ext 4 I'd recommend the following:

<script type="text/javascript">
    LABKEY.requiresExt4Sandbox(true);
</script>
<script type="text/javascript">
    LABKEY.requiresExt4ClientAPI();
    LABKEY.requiresScript('FlowGraph.js');
</script>

<!-- inside of FlowGraph.js -->
Ext4.define('LABKEY.ext.FlowGraph', {...});

<!-- In begin.html -->
<script type="text/javascript">
    Ext4.onReady(function() {

        var flowGraph = Ext4.create('LABKEY.ext.FlowGraph', {...});
    
    });
</script>