Fix permissions in some test and source files.

Remove the executable bit that should have never been set in the first
place.
Split xwalkctl and pkgcmd backend

All the application management (app un/installation) logic is now removed
from it 'xwalkctl'- it is only responsible for XWalk common settings,
like setting of debugging port.

The application management is moved to a separate target: xwalk_backend.
The wrapping script is removed as well.

BUG=XWALK-2671
BUG=XWALK-2579
Merge pull request #2502 from pozdnyakov/split_xwalkctl_and_pkg_backend

Split xwalkctl and pkgcmd backend
Merge pull request #2496 from rakuco/remove-executable-perms

Fix permissions in some test and source files.
Move Chromium 39.0.2171.19, the first M39 beta.

IMPORTANT NOTE:
  When syncing, please make sure you run "gclient sync" TWICE, because
  the first run will remove the src/thid_party/speex directory that was
  moved from an external repository to Chromium itself.
  https://groups.google.com/a/chromium.org/d/msg/chromium-dev/-ozqcZSjd5k/F58XSTZUp7AJ
  has more information on the change.

Most of the commits were just gardening ones to adapt to file location
and API changes in Chromium.

Additional changes worth noting:

* SIMD.js support is temporarily disabled as we always do when switching
  to a new Chromium milestone. XWALK-2734 is tracking this.

* NaCl support had to be disabled for Tizen 32-bit builds because Google
  does not ship a 32-bit NaCl toolchain anymore. XWALK-2679 is tracking
  this.

* We're now tracking Ozone-Wayland's Milestone-Autumn branch.

* Java 7 is now required to build Crosswalk for Android, following the
  requirements from Chromium itself.

* On Tizen, we don't set enable_ozone_wayland_vkb and enable_xdg_shell
  anymore. Since ozone-wayland commit aeb6a5f7 they do not have any
  effect, and one is expected to define whether those features are
  enabled or not with environment variables. We were already setting
  OZONE_WAYLAND_USE_XDG_SHELL in the systemd service file; we now set
  USE_OZONE_WAYLAND_VKB as well.