Christopher,
Thanks for the letter. Its great to meet you. I went ahead and CC'ed the Science Working Group list on this since it has turned into a technical discussion. Setting up meetings is OK to do in private, but we need to keep technical discussions in the open.
I absolutely love the name Triquetrum. I'm an astrophysicist, so I know it well.
I am very glad to hear that you are joining the Foundation. That is really great.
I wanted to address the issues of openness and access that you bring up. First, Eclipse projects are required to use the Eclipse infrastructure, even from the the very beginning, and to have all lists, forums, and bug reports out in the open. Repositories can be on either Eclipse.org servers or Github and most new projects are using the latter. Private communication can happen of course, but the largest part of the discussion must be public. We will find a very cold reception from the community if we are not open.
As far as access to the code goes, the only people who will have commit privileges will be people working on the project, which will most likely be only the people on this list. All contributions from other sources will have to pass through a contribution mechanism such as a pull request or bug report, which requires review by committers and the IP team. So, I wouldn't worry about updates to the core from the perspective of outside developers.
Actual project committers might change things in the code contributed from Ptolemy, - 'Ptolemy core' - but that's their job. Most likely we will have our own parts of the project - even our own high-level cores - that we are developing though. For example, I most likely won't be working on any pieces of Triquetrum contributed from Ptolemy because ICE doesn't use them and I don't know how they work; I'll be working on the service layer and any workflow components above it that directly relate to ICE, like our Item and ItemManager infrastructure if I add that as part of the initial contribution.