Browsing through the log file I cannot see an obvious errors. You seem to have a directory /MarkdownView/.git on the WebDav server which is not in your local file system yet. So all files in that directory tree end up in the the list "Remote new files". However, not a single file is transferred. My suspicion is that this is somehow related to the fact that you try to synchronize a "." (dot) directory. In my script there is a default ignore pattern for dot-files which is apparently in your case not activated since I made a coding error: the default ignore pattern is only added to the list if there is a local ignore file defined which is does seem to be the case in your configuration.
I introduced this ignore pattern since there's currently a limitation in the "working copy" app when it comes to dot files: they cannot be transferred. However, as I can see in your example this does not seem to apply to dot directories, so my pattern is too general. I will try if I can successfully transfer a dot directory and make fixes for that if required.
The real questions, however, is: Why would you want to transfer anything in your .git sub directory? My understanding is that normally this directory only contains technical control files denoting the state of your git project which are better left alone. So far I have used my script to synchronize with three git repositories using "working copy" and in none of them the directory '.git' was visible in the WebDav server at all which is exactly what I would expect from a git client: keeping the scary details away from me. How exactly did you bring all these files into the "working copy" app? Did you do anything else besides "cloning" the git project?