import the repository to be merged in (here reptomerge) as a branch (called tomerge here)

git fetch $path/reptomerge HEAD:tomerge

and merge it in the current master

git merge (--no-commit) tomerge

if there are some conflicting files.F90

git mergetool files.F90

if you want to remove one of the automatically merged files.F90 from the 'add' list and putting it back to the working directory

git reset HEAD files.F90