Do you wish Eclipse would just fix the problem, refresh the file, and let you edit it?
If the answers to these questions are "YES" then I invite you to comment/vote on a bunch of Bugzilla entries that we are discussing these issues on.
Bug 14867 - Don't force me to refresh all the time
Bug 303517 - Update IResource sync state in a timely manner when discovered out of sync
Bug 337446 - Text search should handle out-of-sync resources
