Resolve "synchronize output format between examples"

Closes #576 (closed)

• Adds an applications directory
• Splits examples directory into subdirectories by conceptual topic
• Changes corsika.cpp to c8_air_shower.cpp
• Increased uniformity of examples
• Renames several scripts
• Removed: cascade_example.cpp, cascade_proton_example.cpp, vertical_EAS.cpp
• Added guards for FLUKA so that mars.cpp and water.cpp no longer compile without it
• Added missing override to the getConfig and getSummary calls in some writers to reduce warnings