I've just pushed a change to the future branch that changes the directory
structure to:

app/
    merges/
        android/
        ios/
    www/
    config.xml

As was discussed at our video conference meeting a couple of weeks ago,
this has a number of advantages:
- config.xml is no longer in the www/ directory
- One can easily version control the whole app/ directory, and get their
web assets, merges and so on into the repo.
- That repo can contain additional information: a README.md, supplementary
documentation, tests, whatever. The CLI will ignore anything outside of the
merges and www directories.


The downside is that this is a breaking change: running the new version of
the tools on an old project will fail (but I think in a harmless way) until
you rearrange the directories. You can do that with the following commands:

$ mkdir app
$ mv www/config.xml app
$ mv www app
$ mv merges app

All docs and tests are updated as well. Any problems should be reported on
JIRA and assigned to me.

Braden

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