Saving font, enable GlyphInfo of all glyphs – `Glyphs3-merge` branch

@schriftgestalt
Since a recent change (I guess), saving a GSFont now automatically turns on all the checkboxes from GlyphsInfo for all glyphs! I suspsect this [commit](https://github.com/googlefonts/glyphsLib/commit/96e1bc9cb35e7acc7b704d0868d73423272cd4c6) to introduced this bug

```python
from glyphsLib import *

font = GSFont(".../New Font.glyphs")
font.save()
```

Start by reproducing the reported behavior with the Python snippet and inspect commit 96e1bc9cb35e7acc7b704d0868d73423272cd6. Compare GlyphsInfo checkbox state before and after saving the GSFont; done means saving no longer enables all glyph metadata flags unexpectedly.

Written by the indexing model from the issue text.