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Currently there can be a git status disconnect between eGit and the git repository if the command line is being used. If items are committed at the command line the status within eGit is still showing files that need to be modifed. There is a Team->Refresh option in eGit, but this should really be part of the general Refresh process. So that when a refresh of the workspace is being done, the functionality of Team->Refresh is also run at the same time.
Could reproduce the following: 1. Modify a file using notepad and add it to the index using the command line. 2. After some delay the file is decorated with >*. ">" is wrong since the content of the file does not differ from the content in the index. Reason for the > decoration is DecoratableResourceAdapter taking the time stamp from the (outdated) Eclipse resource instead of taking the real file timestamp.
A fix is proposed at http://egit.eclipse.org/r/#change,1138. Now the dirty marker is determined from the timestamp of the file on disk. If it does not match the content is compared.
Fixed with b50d2355ce2f84c9ce1830b66879859cc70671c0
