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The only trick there is authentication. Otherwise you could put the app in alongside your MODx code -- if your other app is doing any dynamic URL handling, then you’d need to create a separate .htaccess rule.
I’d need to know a bit more about how the app is structured to comment further, but if it all lived on one page (e.g. driven by an index.php page), then you could put the contents of that one page into a MODx page -- just make sure that one page had whatever user permissions required.