we are currently performing some large-scale changes in the Seqan codebase trunk.
This includes line style changes. All text files have their svn:eol-style property set to native now. This means when checking them out, you will get "\r\n" on Windows and "\n" on unices. This hopefully circumvents some problem with line ending consitencies (e.g. you open a file with Unix line endings on Windows with Visual Studio which makes newly inserted line endings Windows line endings.
If you have local changes, you might get conflicts when updating. We hope this will not cause too many inconveniences. However, the step has to be taken sooner or later for the better and the later we do this the more harm it will do.
More information can be found in the SeAn Wiki and Subversion manual