update_layer: fix regressions in missing layer detection

If a layer is removed by its subdirectory being deleted then we want to
pick up on that and produce an appropriate error message - so let the
layer_update code do the checking out and verifying things are correct
before trying to parse layer.conf.

This also fixes --nocheckout still checking out a branch.

Additionally, drop some code that gets the layerbranch which we just
retrieved a few lines above.

Signed-off-by: Paul Eggleton <paul.eggleton@linux.intel.com>

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