I solved the issue with a bit of a hacky scriptlet:
<%
String path = pageContext.getServletContext().getRealPath("/");
Collection<String> paths = new ArrayList<String>();
for (File file : FileUtils.listFiles(new File(path), new String[] { "ext" }, true)) {
//Make the path relative
paths.add(file.getAbsolutePath().substring(path.length()));
}
%>
<c:forEach items="<%=paths%>" var="path">
<jsp:include page="../${path}"/>
</c:forEach>