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chore(deps): bump packages and pin transitive audit fixes
Refresh runtime and toolchain deps to latest, add hono/js-yaml overrides so bun audit is clean, and include a patch changeset.
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.changeset/deps-audit-overrides.md

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"@stainless-code/codemap": patch
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Refresh runtime and toolchain dependencies (better-sqlite3, oxc-parser, oxfmt, oxlint, and related dev tooling) to latest compatible releases. Pin transitive hono and js-yaml to patched versions so dependency audits report no known vulnerabilities.

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