Eclipse STS re creates folders every time it is opened, may be due to file permissions
I was also facing the same issue. To resolve it I did the following steps.


Extract the tar/zip file anywhere you want.
Drag the STS.app file to "Applications".
Now you will see the STS application in launchpad also.
Now you can start STS by clicking on this STS icon from launchpad/spotlight search.


It should resolve the issue.