"Remote System Explorer Operation" causing freeze for couple of seconds

Here are the steps:

1. Click on the Windows > Preferences menu
2. Select General > Startup and Shutdown in the tree
3. Uncheck RSE UI
4. Select Remote Systems in the tree
5. Uncheck Re-open Remote Systems view to previous state
6. Restart Eclipse

Note: You must have Eclipse 4.3.1 (or newer) due to a bug on previous version

Here are the steps:

1. Click on the Windows > Preferences menu
2. Select General > Workspace > Build Order in the tree
3. Uncheck Use default build order
4. Select RemoteSystemsTempFiles
5. Click Remove Project
6. Click Apply and Close

This was driving me crazy too.

Thanks to this topic I got to understand it was the plugin RSE, but I could not uninstall the Remote System Explorer plugin tool either. I had to remove all the plugins whose name started by org.eclipse.rse in plugins/, it's working now.