hint: after resolving the conflicts, mark the corrected paths

This means that you need to explicitly tell Git that you've resolved a conflict at each file or folder (that is path).

Showing the list of yet unresolved conflicts:

git status

Marking a conflict as resolved.

File or all files in a folder should be left and all conflicts are resolved:

git add

File or folder should be removed:

git rm

Next step:

git commit

because some files are in conflict ,you can type git status to find out what is the file with conflict, and after the conflict was sovled ,just git commit -m sth log ,at last git cherry-pick your-commmit-id . see details http://wiki.koha-community.org/wiki/Using_Git_Cherry_Pick#Resolve_conflicts