Set preferences are, by default, set in the context in which they are defined.

For example, if a preference is set at the "user" level and the user changes
the value via UI, the preference will be changed at the "user" level. If it's
set in a .brackets.json file, the preference will be changed there.
If the preference is defined only at the "default" level, it will be set
at the next higher level of precedence ("user" level in our setup).

This is a fix for #6595.
Maintain the original line endings in preferences files
Changes based on review comments
Better doc comment for `Scope.set`
Merge pull request #6602 from adobe/dangoor/6595-pref-set

Fix for 6595: Set preferences are, by default, set in the context in which they are defined