Better Features integration

These all should be separate issues. Regarding 1-3:

1. Flags exported as Features are added to the DB. can they live only in code, like other exports do?

No, because Flags have abilities that other exports do not. Views, Panels, ImageCache presets and other things only have a concept of "overridden" and "default", but no concept of certain properties being "locked" while others may be edited by administrators. This is intentional functionality of the Flag module so that you can lock things like the flag name and link type, but allow administrators to change the link text or confirmation messages. That way other modules can ship with default flags that they can depend on certain functionality.

2. when you change a Flag that was added to a Feature, you can't revert back to the default code. missing UI link at /admin/build/flags. also, a bug? #1117502: Reverting features with flags leaves the feature in overriden mode

Let's leave that to the other issue.

3. when you disable a Feature that adds Flags, the flags remain in the DB (see 1.). they don't get deleted.

That sounds like a bug, let's make a dedicated issue for it.

4. you should not be able to delete a Flag that was added by a Feature, as they should like in code (see 1).

You can't actually delete a flag added by a feature, "deleting" it will merely reset it back to the defaults (afaik).

5. store and export Roles with their names (or machine names provided with UUID), not IDs: #1204918: Export roles as names rather than IDs

Let's leave that to the other issue.

Making a big "multi-issue" like this doesn't help actually solve the problems, since we're not going to try to track 5 different problems in a single issue. Combining issues makes tracking the changes more difficult. If there isn't already and issue for #3, please file a new issue. All other problems already have individual issues or are intentional behavior.