fix: clone empty configuration overrides

[dylan-isaac]

Summary

• clone empty mutable containers during iterative user-config override merging
• preserve shared references in the cloned result without mutating the caller's override graph
• release the regression fix as 0.2.31

Verification

• uv run pytest tests/unit -q (766 passed)
• uv run pytest tests/integration -q -m integration (2 passed)
• uv run ruff check src tests
• uv run ruff format --check src tests
• uv run --extra docs mkdocs build --strict
• git diff --check

Follow-up to #121 and v0.2.30. Refs #65.

[dylan-isaac]

@codex review

Please review head cbc5df52e1ed72d6abf73c720e283317bf432c88, particularly empty/nested/shared mutable override cloning and graph identity/performance compatibility.

[chatgpt-codex-connector]

Codex Review: Didn't find any major issues. 🎉

Reviewed commit: cbc5df52e1

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[dylan-isaac]

@codex review

Please review current head c4e47fdac7cc86762fb014d2e2d07a15deb843cb. This supersedes the earlier review after resolving fresh Ruff 0.16 CI compatibility while retaining the empty-container graph-cloning fix.

[chatgpt-codex-connector]

Codex Review: Didn't find any major issues. Bravo.

Reviewed commit: c4e47fdac7

ℹ️ About Codex in GitHub

Your team has set up Codex to review pull requests in this repo. Reviews are triggered when you

• Open a pull request for review
• Mark a draft as ready
• Comment "@codex review".

If Codex has suggestions, it will comment; otherwise it will react with 👍.

Codex can also answer questions or update the PR. Try commenting "@codex address that feedback".

[dylan-isaac]

Final exact-head review disposition for c4e47fdac7:

• Specification review: PASS.
• CI/release review: PASS.
• Adversarial graph review found pre-existing O(N²) traversal for N aliases to one size-N non-empty list.
• Controller reproduced identical traversal counts and timings on origin/main and this PR head.
• Independent adjudication: PASS: out-of-scope follow-up; the hotfix changes only empty-container clone marking, preserves required identity/isolation semantics, and does not introduce the performance behavior.
• GitHub Codex found no major issues on this exact head.
• All required GitHub checks are green.