I've created a simple SharePoint 2013 application and have setup:
<%@ Page Inherits="Microsoft.SharePoint.WebPartPages.WebPartPage, Microsoft.SharePoint, Version=15.0.0.0, Culture=neutral, PublicKeyToken=71e9bce111e9429c"
MasterPageFile="~masterurl/default.master" Language="C#" %>
However, I've a publishing site with a custom master page setup as default and custom. This master page is now reflected when I go to the application within the site. Note, this is an Office 365 tenant.
Maybe you need to forcibly designate the app#0 webtemplate to be used? see blogpost: http://community.zevenseas.com/Blogs/Akhilesh/Lists/Posts/Post.aspx?ID=11
This blogpost refers to the following msdn documentation: http://msdn.microsoft.com/en-us/library/fp179925.aspx#TypesOfSPComponentsInApps
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