Rob Winch (Migrated from SEC-1909) said:
A number of users have complained about the deprecation warnings in STS. It would be good to update the namespace so that these warnings do not appear (such warnings tend to clutter the workspace and make it hard to find real problems)
In my case, if I remove spring nature for my project, the warnings disappears.
Concretely, I deleted this line from the .project file:
Then refresh&clean project; and cut and paste xml content.