fix: resolve F821 undefined name violations, remove per-file-ignores

[ericchansen]

Summary

Resolves all 33 F821 (undefined name) violations across 3 files and removes the entire per-file-ignores section from pyproject.toml.

Changes

q2mm/parsers/jaguar.py — Initialize current_structure and temp_eigenvectors before the parsing loop. These were assigned inside conditional blocks but used outside them; works at runtime but ruff couldn't verify the control flow.

q2mm/parsers/macromodel.py — Initialize bonds, angles, torsions, atoms, current_structure before the main loop in MacroModel.structures, and col_nums, elements, row_num before the word loop in MacroModelLog.hessian. Same scoping pattern.

test/test_linear_algebra.py — Replace dead code in test_last (already @unittest.skip) with pass. The method referenced log and min_hessian that were never defined — genuinely incomplete refactoring.

pyproject.toml — Remove entire [tool.ruff.lint.per-file-ignores] section. Also removed 3 stale entries (gaussian.py, mol2.py, structures.py) that had zero violations.

Verification

• ruff check . — all checks passed
• ruff format --check — all files formatted
• 421 tests passed, 83 skipped

Closes #128

[Copilot]

Pull request overview

This PR removes all remaining Ruff F821 (undefined name) violations by making variable initialization explicit in a few legacy parsers/tests, allowing the repository-wide removal of Ruff per-file-ignores for F821.

Changes:

• Initialize previously conditionally-assigned locals in JaguarOut.import_file() and MacroModel.structures / MacroModelLog.hessian so Ruff can prove they’re defined.
• Remove incomplete/undefined-reference code from a skipped legacy unittest (test_last) to eliminate F821.
• Delete the entire Ruff [tool.ruff.lint.per-file-ignores] section from pyproject.toml.

Reviewed changes

Copilot reviewed 4 out of 4 changed files in this pull request and generated no comments.

File	Description
q2mm/parsers/jaguar.py	Initializes current_structure / temp_eigenvectors before the parsing loop to satisfy F821.
q2mm/parsers/macromodel.py	Initializes structure-accumulator locals in .structures and Hessian parsing locals in .hessian to satisfy F821.
test/test_linear_algebra.py	Removes undefined-name references from an already-skipped test to eliminate F821.
pyproject.toml	Removes Ruff per-file-ignores now that F821 issues are resolved.

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