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This gets rid of the 'sources' directory and allows all sources
of a given Android application to be in the same directory tree
without using a symlink trick.

Note that apps/<name>/Application.mk is still required though.
A later release of the NDK will get rid of it too, but the change
is too drastic for the upcoming release.

The change moves various source files from sources into their
app/<name>/project/jni directory as well.

The whole documentation is updated to reflect the change.