I'm referring to this "feature" https://developer.blender.org/T45900
It was not happening before, but it is now, and it is messing up the structure of some folders I previously created. Is there a way to disable it?
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This bug was fixed (at 2015-10-15), so the easiest solution is to download nightly build of Blender: https://builder.blender.org/download/ . I have tried it and now I finally can save my files as usually. The fix also will be available in 2.76a and later releases. Alternatively, you can build Blender yourself. The bug was fixed by this patch: https://developer.blender.org/rB767d3f23b7efb4e993574c29ebbbe0a4d90f5e50 .