ALLJOYN-2441 Cleaned up SConscript now that we have a smarter Doxygen builder

Since the Doxygen builder now builds up a list of dependencies and targets when
building html output we no longer have to make dummy targets and we no longer
need to manually add the output directory to the list of items that are cleaned.

The files are now built directly into the dist directory.  This is specified in
the OUTPUT_DIRECTORY option in the Doxygen configuration file.

Change-Id: I40e2f3582592e204fb1022c5c1726c20a649e41c
ALLJOYN-2441 Address error building documentation

When the Doxygen builder is run using cygwin it is messing up the directory
paths. For this reason we can not build the documentation directly into the
distribution directory when building the documentation for unity.  We will
have to build the documentation in place and copy them into the distribution
directory.

Change-Id: Ib0fe3a816d471371e41ff98cad676fc3e62af0a1