Git support does not handle files with accented characters correctly, declaring them as new. See e.g spec/fixtures/subdir/áccéntéd.svg in atom/markdown-preview or lloeki/svg-preview plugins.
Steps to reproduce:
$ git clone https://github.com/lloeki/svg-preview $ cd svg-preview $ atom .
Notice that there’s a file marked as new in the tree view —
However, I can’t reproduce this issue with the markdown-preview repository which has a file with the same name.