Include base pyproject when initializing cache settings

[charliermarsh]

Summary

Regression from https://github.com/astral-sh/ruff/pull/9453/files#diff-80a9c2637c432502a7075c792cc60db92282dd786999a78bfa9bb6f025afab35L482.

Closes #9478.

Test Plan

rm -rf .ruff_cache
cargo run -p ruff_cli -- check ../foo.py

Failed prior to this PR; passes afterwards. The file must be outside of the current working directory, and must not have a pyproject.toml in any parent directory.

[codspeed-hq]

CodSpeed Performance Report

Merging #9480 will improve performances by 4.55%

_{Comparing charlie/resolver (1fd067d) with main (55f8f3b)}

Summary

⚡ 1 improvements
✅ 29 untouched benchmarks

Benchmarks breakdown

	Benchmark	main	charlie/resolver	Change
⚡	parser[numpy/ctypeslib.py]	12.8 ms	12.2 ms	+4.55%

[github-actions]

ruff-ecosystem results

Linter (stable)

✅ ecosystem check detected no linter changes.

Linter (preview)

✅ ecosystem check detected no linter changes.