Navigate to a subdirectory of your project and start Gradle without arguments (e.g. to have a daemon running):
$ gradle
Observe that it creates .gradle subdirectory in the current directory. As a result, if you launch it from various places, your filetree gets polluted with useless .gradle everywhere.
Note that this newly created .gradle contains only a couple of empty subdirectories and no files at all, i.e. it doesn’t appear to be really needed for anything.
Tested with Gradle 2.7 and 2.8.