I started using TFS Team explorer 2012 and happen to notice a new process called promoting. As I understand it, the Team Explorer detect any changes made to the files outside of the TFS explorer and count them for promotion? Am I right?
How do I take care of the situation where I made a change to the file which is already checked out through TFS, then made a change via Windows Explorer\Notepad but dont want to include the changes made through the Windows Explorer\Notepad.
While everything that discens said is correct, one thing bears explicit mention: there is no change to the level of granularity of Team Foundation Server. You still check out files and edit files and check-in files.
In your example, if you have a file checked out and you edit it in Notepad, the changes will be checked in. There is no change here from previous behaviors. There is no way to keep these changes from being checked in, short of saving the file with a different file name.