Fix for inheritance problem exposed in examples

[lhstrh]

• Fix problem in Examples failing playground-lingua-franca#53
• Fix Inheritance not working with fedgen #1733
• Add comments to tests
• Clean up FederateInstance

[edwardalee]

I'm confused about the use of the word "inherits" here. You changed all the contains methods to inherits with comment changes like this: from

   * Return true if the specified timer should be included in the code generated for the federate.
    * This means that the timer is used as a trigger in a top-level reaction that belongs to this
    * federate. This also returns true if the program is not federated.

to

    * Return {@code true} if this federate inherits the given timer.

But these don't mean the same thing. Inheriting a timer means that the timer is defined in a class that this reactor extends. But that does not seem to be what is being checked. Perhaps a different word is needed here?

[edwardalee]

LGTM, modulo some suggestions on comments and reintroducing initialization of local variables.

[lhstrh]

The PR was already on auto-merge, and your approval pushed it onto the merge queue. Next time, when making suggestions, please hit the "request changes" button, not the "approve" one :-) ...I can create a separate PR to make your suggested changes to the comments.

[lhstrh]

The PR was already on auto-merge, and your approval pushed it onto the merge queue. Next time, when making suggestions, please hit the "request changes" button, not the "approve" one :-) ...I can create a separate PR to make your suggested changes to the comments.

Alternatively, we could enable a feature that requires all conversations to be resolved prior to merging. I think it might be a good idea because that gives reviewers the ability to approve and still give suggestions for (optional) changes.