fix(deps): refresh Python dependencies

[harumiWeb]

Summary

• Upgrade the complete Python dependency lock for the root and benchmark workspace members within the existing Python and package constraints.
• Update packages covered by all 43 currently open Dependabot alerts to patched versions.
• Refresh the frozen Ruff and mypy pre-commit hooks to 0.16.9 and 2.3.1.
• Adjust internal typing compatibility for the updated mypy and xlwings type surfaces without changing runtime or public API behavior.
• Keep Ruff formatting limited to Python-family files and align the mypy hook with the configured src/exstruct/ target.

Tests

• uv lock --check — passed.
• uv sync --locked --all-packages --all-groups --all-extras — passed.
• uv run task ruff, uv run task mypy, and uv run task precommit-run — passed.
• uv run task build-docs — passed; MkDocs emitted a navigation warning for generated/models.md.
• Full pytest suite not run.
• GitHub still reports 43 alerts on main; those alert states will update after this PR is merged.

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Summary by CodeRabbit

• Chores
  • Updated code-formatting and type-checking tools and their coverage across the project.
  • No end-user-facing behavior changes were made.
• Documentation
  • Added project records outlining maintenance work and verification status.

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ℹ️ Recent review info

⚙️ Run configuration

Configuration used: defaults

Review profile: CHILL

Plan: Advanced

Run ID: f97c3901-339c-477e-aa50-7a0de54e573b

📥 Commits

Reviewing files that changed from the base of the PR and between 92bc120 and d9758ec.

⛔ Files ignored due to path filters (1)

• uv.lock is excluded by !**/*.lock

📒 Files selected for processing (11)

• .pre-commit-config.yaml
• src/exstruct/core/pipeline.py
• src/exstruct/core/shapes.py
• src/exstruct/edit/internal.py
• src/exstruct/edit/specs.py
• src/exstruct/render/__init__.py
• tasks/feature_spec.md
• tasks/todo.md
• tests/conftest.py
• tests/mcp/patch/test_models_internal_coverage.py
• tests/render/test_render_init.py

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📝 Walkthrough

Walkthrough

The pull request updates Ruff and mypy pre-commit hooks, documents the dependency refresh, and adjusts typing-related code and formatting. The summarized source and test edits do not change runtime behavior.

Changes

Python dependency refresh

Layer / File(s)	Summary
Refresh scope and hook revisions tasks/*.md, .pre-commit-config.yaml	The task records describe the dependency refresh, verification, and 128 resolved packages. They also record that 43 Dependabot alerts remain open pending merge. The pre-commit configuration updates the Ruff and mypy revisions and hook file selection.
Typing compatibility and formatting src/exstruct/core/*, src/exstruct/edit/*, src/exstruct/render/__init__.py, tests/conftest.py, tests/mcp/patch/test_models_internal_coverage.py, tests/render/test_render_init.py	Source edits adjust type casts and format conditions and error messages. Test edits reformat annotations and callbacks. The summarized behavior remains unchanged.

Priority: ➖ Normal

Estimated code review effort: 2 (Simple) | ~10 minutes

Change: Other

Merge Risk: ⚪ Minimal · up to d9758

The dependency and tooling refresh shows no concrete user-facing behavior regression. Reported checks passed, though the full pytest suite was not run; no actionable merge blocker is established.

🚥 Pre-merge checks | ✅ 5

✅ Passed checks (5 passed)

Check name	Status	Explanation
Title check	✅ Passed	The title clearly and concisely identifies the Python dependency refresh, the main change in this pull request.
Description check	✅ Passed	The description explains the dependency refresh, scope, compatibility constraints, and validation results. It omits the template’s Acceptance Criteria section and some checklist items, but the descrip…
Docstring Coverage	✅ Passed	Docstring coverage is 92.31% which is sufficient. The required threshold is 80.00%. Docstring coverage is scoped to functions touched by this diff. Analyzed 13 functions across 8 files. (3 skipped: 3 …
Linked Issues check	✅ Passed	Check skipped because no linked issues were found for this pull request.
Out of Scope Changes check	✅ Passed	Check skipped because no linked issues were found for this pull request.

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Up to standards ✅

🟢 Issues 0 issues

Results:
0 new issues

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🟢 Metrics 0 complexity · 0 duplication

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Complexity	0
Duplication	0

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