Function apply_rule_severities 

pub fn apply_rule_severities(
    results: &mut AnalysisResults,
    config: &ResolvedConfig,
)

Remove findings whose effective severity is Off from an analysis result.

Every surface that reports findings runs this pass: the check command (which also serves dead-code and the CLI audit), the editor analysis path behind inline diagnostics and the sidebar, and the programmatic runtime behind the MCP tools, the decision surface and the Node bindings. Each of them runs it at the same two points, once over the freshly analyzed set and once after type-aware reconciliation, because reconciliation can append findings. The pass removes findings and writes the gate severity of each finding that stays, so the second run is idempotent when nothing was appended.

When overrides are configured, per-file rule resolution is used for file-scoped issue types. Circular dependencies resolve against every file in the cycle. Non-file-scoped issues (unused deps, unlisted deps, duplicate exports) use the base rules only.