fix(#172): eliminate shell() calls in audit-workspace and session-handoff#204

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fix/172-shell-cleanup-remaining

Commits on Mar 10, 2026

fix: replace shell syntax in run() calls across 8 tools (#172)
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fix: replace shell syntax in run() calls with array args or shell()
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fix(#172): replace shell() with Node.js APIs in audit-workspace and session-handoff
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