Hi shoab shah,
your custom application will also need to rely on ADFS and is a webresource Iframe in CRM. What I can tell is that currently I have investigated a lot of time in adfs 2012R2 (adfs3.0) and it seems that Microsoft forgot to publish a KB for it because there
is a windows auth prompt when accessing the webresource iframe (customwebapp) after the credentials prompt of adfs. If you plan to use adfs 2012R2 and no option to use adfs 2 you will have this extra prompt, it seems that Microsoft will not publish a fix for
that in short future, but I hope so because we are using adfs 3 and can´t move back.
This article also for 2013 and also 2015 https://msdn.microsoft.com/en-us/library/gg509057%28v=crm.5%29.aspx except if youre using VS2015 than you must create manually the relying trust without XML or you use the XML from crm before appling crm relying trust
and than remove the XML and update automatically mark and change the identifiers manually.
gruss Daniel Ovadia MBSS - Microsoft Dynamics CRM MCNPS
