Finally solved the problem, based on solution used in following thread:
http://stackoverflow.com/questions/19475387/how-to-handle-fix-git-add-add-conflicts/20626817#20626817

# Deleted all files from the local workdir.

rm -rfv myconflictedfolder


# commit this change

git commit -m 'Resolve git Add/Add branch merge conflict by deleting conflicted 
folder and files in myconflictedfolder'


# do merge from remote 

git pull origin master


Pull was executed successfully.


Best regards,
Konrad


2015. május 16., szombat 14:37:28 UTC+2 időpontban Philip Oakley a 
következőt írta:
>
>  
> *From:* Konrád Lőrinczi 
>
> *To:* git-...@googlegroups.com 
> *Sent:* Saturday, May 16, 2015 1:03 PM
> *Subject:* [git-users] Merge conflict error, when there was no change in 
> mentioned file
>
> I have a site local repo and a remote repo.
> Local repo contains the 1-2 month old content of remote repo.
>
>
> I try to pull the whole content into local repo.
>
>      git pull origin master
>     From ssh://.../site.git
>      * branch            master     -> FETCH_HEAD
>     ...
>     CONFLICT (add/add): Merge conflict in admin/process_email.php
>     Automatic merge failed; fix conflicts and then commit the result.
>
>
>
> I checked process_email.php using P4Merge, but shows no conflict, 
> furthermore there were no changes at all, no difference.
>
>
> I get 
>
>      $ git status
>     On branch master
>     nothing to commit, working directory clean on both repos. 
>
>
>
> Also I tried 
>
>      $ git pull -X theirs origin/master master
>
>
> But still get the same error.
>
> I want to merge the remote origin repo with my local repo.
> I want to overwite local repo with remote origin repo content as the 
> remote repo is newer, contains the latest code.
>
> More than 2000 files are conflicting, while I checked the conflict and 
> they have the same content. I would not want to do manual conflict 
> handling. 
>
> I have 
>  autocrlf = False
> in the .gitconfig.
>
>
> Why do I get conflict error for files, which have exactly the same content?
>
> Konrad,
>  
> An easy way to see what is going on is to split the 'git pull' into 'git 
> fetch' (*) and then 'git merge' (*).
>  
> You may need extra options on the fetch and merge depending on your 
> version to select the branches you want from the remote server into your 
> remote-tracking branches (rtb) for that server.  
>  
> This separates out the issues and once you have all the remote changes 
> held locally in your rtb's you can more easily do diffs between the two 
> branches.
>  
> It can be quite a mind-wrench when you grok that rtb's are just local 
> branches with a convenient name, rather than someting special that's to be 
> 'feared'.
>  
> You may find that there are 'end of line' differences between the commits 
> in the server, and the commits you have locally, which after eol 
> conversion, look identical, but the different eol strings makes the sha1's 
> different.
>  
> --
>  
> Philip
>  
>

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