Issue 641466 has been merged into this issue.

 Issue 673525  has been merged into this issue.

 Issue 673525  contains specific repro steps for an example case. Changing this to a bug given the poor user experience.

The following revision refers to this bug:
  https://chromium.googlesource.com/chromium/src.git/+/1f9c06b2bc825d86db2fbc2b21dc35fd453f8b69

commit 1f9c06b2bc825d86db2fbc2b21dc35fd453f8b69
Author: tiborg <tiborg@google.com>
Date: Thu Jan 19 19:23:03 2017

VR Shell does not redirect to another app while in VR mode.

- VrShellImpl sets a custom TabRedirectHandler implementation to the tab displaying the vr shell.
- The custom TabRedirectHandler implementation prevents any redirect to another app, e.g. when clicking on youtube.com.

BUG=670128

Review-Url: https://codereview.chromium.org/2641933002
Cr-Commit-Position: refs/heads/master@{#444814}

[modify] https://crrev.com/1f9c06b2bc825d86db2fbc2b21dc35fd453f8b69/chrome/android/java/src/org/chromium/chrome/browser/tab/Tab.java
[modify] https://crrev.com/1f9c06b2bc825d86db2fbc2b21dc35fd453f8b69/chrome/android/java/src/org/chromium/chrome/browser/vr_shell/VrShellImpl.java

Tibor's patch was the first step towards addressing this issue, but more work is needed for the 'optimal' experience. Namely, if a url would direct to an app that supports VR, we should allow chrome to launch that app in VR rather than just rejecting.

Looking at the last comment, what's left here doesn't look like a bug anymore. We'd need a list of VR apps that can be launched from websites to increase priority.