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On my subversion client (cornerstone), when connecting to a new SVN repository I have 3 options: File repository, HTTP Server and SVN Server.
Is the difference only in the protocol used to communicate ?
Yes. SVN can be accessed through HTTP/WebDAV with the mod_dav_svn Apache module. Other than the protocol difference, it supports the same operations.
You can read more about this configuration in the Subversion book.