Since the introduction of many enhancements in the IDE, such as the Boards Manager, and the Arduino Builder system, it was decided that this would break backwards compatibility with older versions of the IDE. In version 1.5.0 of the IDE it was therefore decided that the location of all the Arduino data files (of which there are now many, not just a
preferences.txt file) should be moved to a new location, and
.arduino15 was chosen to reflect the current version.
Since then a version number war broke out between the two Arduino factions, which was then subsequently resolved, and we ended up with the 1.8.x group of versions. These, since they haven't introduced anything drastic to the underlying system since 1.5.x, haven't needed to change the location of the data files (indeed, to do so would be undesirable), so it has remained as
I don't believe it's possible to change the preferences location, since the only place would be in preferences, and it would need to load the preferences to know where to load the preferences from.
If you really need to access the
preferences.txt file yourself as
~/.arduino/preferences.txt (why would you?) then you can just delete the old
.arduino directory and create a link to the new one:
$ rm -rf .arduino
$ ln -s /home/pi/.arduino15 .arduino
There is a command-line argument to the Arduino IDE that lets you set the location of the preferences.txt file (detailed here):
$ arduino --preferences-file /home/pi/.arduino/preferences.txt
However what that will do with an old preferences.txt file is anyone's guess.