What I am mostly concerned about is keeping this whole forking "Kosher": I don't want the new code that will coexist and be intertwined with the old code to somehow fall under the umbrella of the preexisting IP contention because I messed up on my due diligences with license language and what not.
CAUTION: I AM NOT A LAWYER. But I think I can probably steer you in broadly the right direction nonetheless.
You own the copyright to the new code that you write on your own dime. Nothing can restrict your right to do what you like with your code, short of selling or otherwise assigning the copyright to someone else. The license you release
your code under is your grant of a license to
other people; it tells other people what they are allowed to do with your code. But you are always free to do what you like with your code - including relicense it under different terms - since you own it.
(EDIT: rewritten this para) The things you have to worry about are that you don't end up using code that ATI owns contrary to any license grant. And secondly that you don't end up releasing a product that it is effectively impossible for anyone to run without using code that ATI owns contrary to any license grant. At the moment, the only license grant for the ATI-owned code is the GNU Affero GPL it was publicly released under, but of course you're always free to try to negotiate some more permissive license grant with ATI.
I'm very dubious of your plan to manage copyright at the level of commits - i.e. one copyright and license up to a particular commit, and another for subsequent commits. This is very unconventional and sounds like a recipe for legal confusion. You can't meaningfully pick apart the commits to a single file. Don't try to do this without advice from a lawyer. 0.93.3 files that you modify should instead be treated as derivative works, IMHO. The way I'd proceed is as follows.
The way I see it, you have three types of files.
1. Files from 0.93.3 which you haven't modified. Keep the copyright notice and license unchanged on these files. These files are owned and licensed by ATI. Obviously over time there will be fewer of these; that's fine.
2. Files from 0.93.3 that you have modified. These files are derivative works of ATI's work, and both you and ATI have copyright claims on them. Keep these files under the GNU Affero GPL, but update the copyright notice to include both your copyright claim and ATI's. You can't relicense these derivative works except in accordance with ATI's license grant. Fortunately the GNU Affero GPL allows you to create derivative works provided they are licensed on the same terms.
3. New files that are entirely your own work, on your own dime. You own the copyright on these files, so you are technically free to release these under any other license you choose - but if this license you choose were incompatible with the GNU Affero GPL then it may be impossible for anyone to legally comply with all the licenses. Any license that is compatible with the GNU Affero GPL is fine here, so a permissive license such as the MIT license should be absolutely fine. These new files should contain just your copyright notice and the relevant license (and no reference to ATI).
Your LICENSE file should then simply indicate that portions are copyright ATI and portions are copyright you, and that furthermore portions are licensed under the GNU Affero GPL and portions are licensed under the MIT license, and include the text of both licenses for reference. It should instruct people to refer to individual source files to find out the copyright and license that applies to those files. EDIT: I'd rename the existing LICENSE file to LICENSE-ATI or LICENSE-0.93.3 or some such, and leave it unchanged except for a some added text at the beginning saying this was the license under which ATI released 0.93.3. I'd then reference the LICENSE-ATI file from your new LICENSE file, too, and indicate that this was the license under which the ATI-owned code was orignally released. This is useful for reference, and it also avoids breaking the reference in the ATI copyright messages to see the LICENSE file.
Obviously, you want to aim to modularise things in such a way as to maximise the number of files that fall into category 3 - but of course you have to be careful when refactoring not to accidentally move pieces of ATI-derived code into your category 3 files - or at least, if you do, you should recategorise those files as category 2.
I'm pretty sure what I describe above is safe, and is the most sensible way to proceed, but once again IANAL. Happy to answer questions, though, if any of the above is unclear. EDIT: And of course happy to review and comment on your updated license/copyright notices.
Regards,
roy
EDIT: Significant edits to the above - you may want to reread.
EDIT: Further edits to the advice on LICENSE files.