chore: remove unused dependencies

[SkyeAv]

Removes unused runtime/docs dependency declarations and refreshes uv.lock so installs pull a smaller dependency set without changing source behavior.

Dependency Cleanup

• Runtime deps: removes unused jsons, openai, ipykernel, and the direct click entry from the mcp extra in pyproject.toml.
• Dev deps: added jupyter and ipykernel to dev dependencies in pyproject.toml.
• Deduplication: removes the duplicate networkx declaration while keeping the active networkx dependency.
• Docs deps: removes unused furo and sphinx_markdown_builder; docs still build with the configured alabaster theme.
• Lockfile: refreshes uv.lock, dropping the now-orphaned transitive packages from the removed dependencies.

Testing

• uv lock --check → resolved successfully.
• uv run --all-extras pytest tests/ -q → 58 passed, 1 skipped.
• Temp-venv docs install/build with docs/requirements.txt + make -C docs html → build succeeded with existing docs warnings.
• uvx deptry . --ignore DEP001 → no remaining unused-dependency findings.
• uv run --all-extras ruff check . && uv run --all-extras ruff format --check . → fails on existing source lint issues outside this PR’s dependency-only scope.