..$ rails s => Booting WEBrick => Rails 4.0.4 application starting in development on http://0.0.0.0:3000 => Run `rails server -h` for more startup options =>
Simple:
go in the root folder of the project when this happens and run:
gem install shutup shutup
This will find the process currently running, kill it and clean up the pid file
NOTE: if you are using rvm install the gem globally
rvm @global do gem install shutup