If you open an existing OTF or a TTF, and you save, the system assumes you want overwrite the original file. This is an issue only in some versions, but be careful anyway and always work with a copy.
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).
I just did the following with Glyphs beta 1.3.19 (452):
Open a fontname.otf file using “open fontname.otf” from the Terminal command-line while Glyphs was already open.
Selected a glyph in the Font View.
Selected Layers -> Correct Path Direction
Undo doesn’t matter here. Even when selecting Undo, the file still shows as “Edited” (though, perhaps that’s to do with the change to a .glyphs file).
At that point (right after Correct Path Direction), the file immediately becomes “fontname.glyphs” (with the original .otf being removed). fyi.