Thanks a lot! Great explanation.
I use to create a special folder called 'Notes' for the ODP inside the git repo, and I started to implement Dora after check this Notes in 9 video: (thanks Paul!)
http://notesin9.com/index.php/2014/03/24/sourcetreedeepdive/
Watching the video I realized Paul creates a 'notes' folder for the ODP and then when Dora is installed, .gitignore is pointing to several “familiar” files inside 'nsf/', so here's where my confusion started.
I did several tests, and I also realized that even changing the .gitignore paths from 'nsf/' to 'Notes/' the files were still tracked by git, you can imagine my mess (it was because they had been added to the repository previously, as you explain)
Finally, I suppose it's necessary to install Dora in a repo BEFORE the first commit of the ODP, so the files (.classpath, .project, plugin.xml,…) listed in the .gitignore can be ignored properly by git, or at least do not track them before .gitignore is ready.
Thank you very much for your support!