Remove deprecated permissions functions from Extension

      The methods GetActivePermission() and HasAPIPermission() have been deprecated
for more than a year.  Finally remove them.
Also clean up some includes in extension.h, and fix transitive includes.

BUG=379356
TBR=atwilson@chromium.org (c/b/background)
TBR=yurys@chromium.org (c/b/devtools)
TBR=bauerb@chromium.org (c/b/managed_mode)
TBR=dalecurtis@chromium.org (c/b/media)
TBR=dewittj@chromium.org (c/b/notifications)
TBR=msw@chromium.org (c/b/ui)

All TBRs are for strictly mechanical changes - no functional difference.

Review URL: https://codereview.chromium.org/314113010

git-svn-id: svn://svn.chromium.org/chrome/trunk/src@275531 0039d316-1c4b-4281-b951-d872f2087c98