chore(ci): lint the whole repo, fix pre-existing alembic errors (#352)

[Vignesh-P-C]

Description

CI only linted server/ and tests/; alembic/ and scripts/ were
never checked and had drifted — running ruff check . finds 2 real
pre-existing errors (an unused import in a migration file, and a
deliberate-but-unflagged E402 in alembic/env.py). CONTRIBUTING.md
tells contributors to run ruff locally without qualifying the path,
so anyone running the obvious ruff check . hits 2 failures on a clean
checkout and has to work out they're pre-existing. This fixes both
errors and widens CI to lint the whole repo.

Related Issue

Closes #352

Type of Change

• 🐛 Bug fix (non-breaking change that fixes an issue)
• ✨ New feature (non-breaking change that adds functionality)
• 💥 Breaking change (fix or feature that would cause existing functionality to change)
• 📚 Documentation update
• 🔧 Maintenance (refactoring, dependencies, CI, etc.)
• 🧪 Test improvement

Changes Made

• Removed the unused import sqlalchemy as sa in alembic/versions/0014_query_embedding_cache.py
• Added [tool.ruff.lint.per-file-ignores] in pyproject.toml for alembic/env.py's deliberate late import (must run after the config comment block that resolves sqlalchemy.url), with a comment explaining why
• Widened the CI lint step from ruff check server/ tests/ to ruff check ., so new top-level directories don't silently go unlinted

Testing

• Unit tests pass locally
• Integration tests pass locally
• Manual testing completed
• New tests added for new functionality

Test Commands Run

ruff check .   # All checks passed!

Checklist

• My code follows the project's coding standards
• I have performed a self-review of my code
• I have commented my code where necessary
• I have updated documentation as needed
• My changes generate no new warnings or errors
• I have added tests that prove my fix/feature works
• All existing tests pass
• I have checked for breaking changes

Screenshots / Recordings

N/A — CI/lint config only. ruff check . output is the proof:
All checks passed!

Additional Notes

Went with ruff check . over explicitly listing scripts//alembic/
alongside server//tests/, per the issue's own reasoning: . stays
correct as new top-level directories get added, where an explicit list
would need updating every time. No test changes needed since this is
lint/CI config only — verification is ruff check . exiting 0, which
it does.

Fixes #352.

[Vignesh-P-C]

The failing check (CI / test) looks unrelated to this PR — the only
failure in the run is test_subject_entities_uniqueness.py::test_concurrent_upserts_converge_to_one_row,
a concurrency test for the #383 subject_entities uniqueness feature
that landed in main after I branched. This PR only touches an unused
import in a migration file, a ruff per-file-ignore, and one CI YAML
line — nothing related to entity uniqueness or concurrency.

I don't have permission to re-run the job myself, so flagging here in
case it's useful — might be worth a look for #383, or could just be a
one-off race under CI load.

[smaramwbc]

Merged — thanks for the clean fix, this closes #352. I verified ruff check . passes repo-wide on the merged tree (including under ruff 0.16.6) and pushed one cosmetic commit restoring the trailing newlines at EOF in the three touched files before merging.