Public release, 2025-10

[brianhenn]

Updates the codebase to a recent commit on full-model (3ef085c).

This PR was created by the following steps, similar to the prior release in July 2025:

• Using the script in full-model to specify which files should be copied over, and filter the git history to only include these files.
• Pushing this filtered repo to a new branch on ace called linear-history-2 (we have to make a new linear history branch every time since different filtered histories are not compatible).
• Creating the release-2025-10 branch on ace, and then squash-merging linear-history-2 into this branch using git merge linear-history-2 --squash --allow-unrelated-histories --strategy-option theirs (necessary because GH will not allow opening a PR with incompatible histories, but --allow-unrelated-histories results in a branch that is "compatible").
• Re-apply deletion of files that had been deleted or moved since last public release, as these are not caught by the merge strategy.
• Removing CI-related items that do not run in the public repo, such as the GPU tests and specific compute system references.