igt/tests: Clear pipes properly in kms_atomic_transition

There is an issue happening from time to time in kms_atomic_transition
(bug #1918). We periodically get assertion that some two outputs
attempt to use same pipe like this:

"Failed assertion: output->pending_pipe != b->pending_pipe"

After some investigation came to conclusion that this is happening
because we are calling igt_output_set_pipe(output, PIPE_NONE) only
for connected outputs, which is wrong.
Periodically igt_display_refresh/igt_output_refresh call calls can
update the output state to disconnected. However that doesn't clear
the pipe being assigned(i.e output->pending_pipe).
So this causes assertion to be triggered on next igt_display_refresh
called during commit.

Bugzilla: intel#1918

v2: - Do not use for_each_valid_output_on_pipe as it also iterates
      only on connected outputs(Maarten)
    - Also fix run_modeset_tests function

Signed-off-by: Stanislav Lisovskiy <stanislav.lisovskiy@intel.com>
Reviewed-by: Maarten Lankhorst <maarten.lankhorst@linux.intel.com>
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