One of the common mistakes done during development is to write runtime data like logs or persistent data in the folder in which the application has been installed. Its may be most convenient to write them in the root directory, but issues arise when the application has to be upgraded. Now as the installation directory also contains runtime data, we are risking loosing important historic information.
Avoid This. Make sure while designing the application, you set aside a folder outside of the root directory to write any runtime data.
Though this seems like commonsense, many a times it is forgotten during the rush.