merge: move messages about possible conflicts a litte earlier I actually wanted to reduce the amount of code around the call to applyupdates(), so I tried moving these warnings a little earlier, and I think it makes the output make a little more sense (see changes to test cases).

.. Common link and substitution definitions.

.. |hg(1)| replace:: **hg**\ (1)
.. _hg(1): hg.1.html
.. |hgrc(5)| replace:: **hgrc**\ (5)
.. _hgrc(5): hgrc.5.html
.. |hgignore(5)| replace:: **hgignore**\ (5)
.. _hgignore(5): hgignore.5.html