As I recall, if you open an existing OTF, make an edit, don't attempt to save and just close the window (the OS X auto-save is causing the actual save, I believe), that the original OTF file will disappear and be replaced by the .glyphs version. When glancing at an OTF, it's safer to make a copy first, right now.
Yes, that exists. Press Option while looking at the File menu. Or, just press Option-Shift-Command-S to save as. Without the Option key, that sequence (Shift-Command-S) is "Duplicate."
Preferences: Expert allows you to disable versions style saving in Glyphs. I heartily recommend doing so. I manually increment my files and just don’t use the .glyphs file extension; instead I name the file fontname.1, fontname.2, and so on.
I fixed this. Can try the latest update (this time correctly labeled as beta).
This is true. Apple changed that between 10.7 and 10.8. But I usually deactivate the "Lion auto save". Unfortunately I had to remove this option in the App Store version.
I usually use a date as file number like "Graublau 130106.glyphs" (YYMMDD). This time I know when I have edited the file the last time (the file creation date is not very reliable).