Use Window instead of RootWindow in many more places throughout the codebase

TBR=sky@chromium.org
http://crbug.com/308843

Review URL: https://codereview.chromium.org/66653005

git-svn-id: svn://svn.chromium.org/chrome/trunk/src@234166 0039d316-1c4b-4281-b951-d872f2087c98
SVN changes up to revision 234166