Add CMake option to enable/disable short file names in Doxygen

Commit 3f363a enabled short file name generation in Doxygen to address
filesystem limitations that arose while packaging PCL. However, for the
purposes of online documentation, short names are not acceptable as they
change with every build. This makes referring to function/class
documentation impossible.

This pull request adds a CMake option `DOXYGEN_USE_SHORT_NAMES` which
affects the corresponding Doxygen option. By default it is set to `OFF`,
i.e. generated file names will be long and descriptive, just like this
used to be prior to the aforementioned commit.
Merge pull request #716 from taketwo/add-doxygen-use-short-names-option

Add CMake option to enable/disable short file names in Doxygen