We have master and a second branch in our repository. We are merging from 
branch to master every few days. Master has almost no new changes at this 
time (other than the merge commits), development is happening entirely on 
the branch. 

The latest merge is failing with a merge conflict. I can fix the merge 
conflict, but there are a lot of other files which do not show any merge 
conflict but have not been updated to the version in the branch. These 
files do show as modified, but they are not in sync with the version of the 
file in HEAD of the branch. 

I am using the following commands: 

> git checkout master 
> git pull --rebase
> git merge origin BRANCHNAME

What can I do to either have git throw merge conflicts for files which are 
different or move them to the version in the branch. 


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