@kevinrabun/judges 3.22.1 → 3.23.2

package/CHANGELOG.md

@@ -2,6 +2,65 @@
 
 All notable changes to **@kevinrabun/judges** are documented here.
 
+## [3.23.2] — 2026-03-04
+
+### Fixed — False Positive Reductions (9 categories)
+- **COST-001 / PERF-001: Sequential Python loops no longer flagged as nested** — Fixed indent-stack algorithm to pop loop scopes on all code lines (not just loop lines), so that `try/except`, `if`, and `with` blocks correctly close preceding loop scopes. Sequential loops inside try/except blocks are no longer misidentified as O(n²).
+- **SWDEV-001-post / MAINT-001-post: Nesting depth threshold raised to 5+ levels** — Changed deep-nesting threshold from 16 spaces (4 levels) to 20 spaces (5 levels), matching `structural-parser.ts`. Python patterns like `async def → try/except → for → if` naturally need 4 levels and should not be flagged.
+- **SWDEV-002-post: `except Exception:` no longer flagged as bare except** — Removed `except Exception:` from `GENERIC_CATCH.python` pattern. `except Exception:` correctly excludes `BaseException` subclasses (KeyboardInterrupt, SystemExit) and is the recommended Python pattern for facade layers.
+- **SOV-001: Docstring body lines no longer trigger sovereignty findings** — Added multi-line Python string tracking (`"""`/`'''`) to the data-sovereignty export keyword scanner. Keywords like "export", "report", "analytics" inside module docstrings are no longer mistaken for real data export paths.
+- **DOC-001: Multi-line Python function signatures now detected** — Extended docstring lookahead to walk past multi-line function signatures (parameters spanning multiple lines) before searching for body docstrings. Previously, functions with signatures spanning 5+ lines would be falsely flagged as undocumented.
+- **MAINT-002-post: Format template strings excluded from duplicate detection** — Duplicate string detection now skips strings containing format placeholders (`{}`, `%s`, `${}`), and strings that are purely whitespace. Template strings repeated in different contexts are no longer flagged.
+- **STRUCT-006: `TYPE_CHECKING` imports excluded from weak type detection** — `detectWeakTypes()` now skips lines containing `TYPE_CHECKING` and all lines inside `if TYPE_CHECKING:` blocks in Python. Static-analysis-only imports are no longer flagged as weak/dynamic types.
+
+### Tests
+- 14 new tests covering all 9 FP categories (both positive and negative cases)
+- 1020 judges tests passing, 689 subsystems tests passing (1709 total)
+
+## [3.23.1] — 2026-03-04
+
+### Fixed
+- **TypeScript type errors** — Fixed 5 compilation errors that caused CI failure on v3.23.0:
+  - `doctor.ts`: Referenced non-existent `judges` and `threshold` properties on `JudgesConfig`; now uses `disabledJudges` and `minSeverity`
+  - `rule-metrics.ts`: Imported `JudgeDefinition` from `evaluators/index.js` which didn't re-export it; now imports from `types.js`
+  - `snapshot.ts`: `Record<Severity, number>` missing `info` key; added `info: 0` initializer
+  - `dedup.ts`: Referenced non-existent `filePath` property on `Finding` type in `findingDiffKey()`
+- **Test fix** — Updated finding-diff test that relied on invalid `Finding.filePath` property to use the `diffFindings()` `filePath` parameter instead
+
+### Tests
+- 1006 judges tests passing, 689 subsystems tests passing (1695 total)
+
+## [3.23.0] — 2026-03-05
+
+### Added — P0: Trust & Accuracy Foundation
+- **Hard/subtle benchmark cases** — 13 new benchmark cases targeting subtle vulnerabilities (prototype pollution, timing attacks, ReDoS, SSRF through URL parsing, null-byte injection, etc.) with `DifficultyResult` interface and strict metrics; `--save` CLI flag for benchmark persistence
+- **Autofix patch expansion** — 33 new patch rules (71→104 total): 25 single-line rules covering CSRF, prototype pollution, ReDoS, path traversal, insecure cookies, etc; 8 multi-line patch rules for complex fixes; 27 new patch tests
+- **V2 baseline with fingerprinting** — Complete `baseline.ts` rewrite (142→~510 lines) with V2 format: per-file fingerprinted findings, `baselineVersion: 2`, `fingerprintBaseline()` with line-context hashing, `diffBaseline()` showing new/fixed/carried findings with severity summaries; 17 new tests
+
+### Added — P1: Developer Experience & Adoption
+- **Sample report generation** — `examples/generate-reports.ts` script producing Markdown, JSON, and SARIF reports; 3 sample reports in `reports/`
+- **PR comment dedup & Check Runs** — Enhanced `action.yml` with deterministic comment fingerprinting to prevent duplicate PR comments, Check Runs API integration via `@octokit/rest`; 6 new tests
+- **Plugin loading infrastructure** — `loadPluginJudges()`, `validatePluginSpecifiers()`, `isValidJudgeDefinition()` in config.ts; `JudgesConfig` expanded with `preset`, `failOnFindings`, `baseline`, `format`, `plugins` fields; `mergeConfigs()` and `resolveJudgeSet()` plugin-aware; 30 new tests
+- **Suppression audit trail** — Full suppression rewrite with `judges-ignore-block`/`judges-end-block` block scope, reason capture, `applyInlineSuppressionsWithAudit()` returning `SuppressionResult` with `SuppressionRecord[]` audit trail; 14 new tests
+- **Team feedback aggregation** — `contributor` field on `FeedbackEntry`, `TeamFeedbackStats`/`RuleTeamStats` interfaces, `mergeFeedbackStores()`, `computeTeamFeedbackStats()`, `formatTeamStatsOutput()`; 16 new tests
+
+### Added — P2: Depth & Precision
+- **Rule test assertion framework** — `RuleTestCase`/`RuleTestResult`/`RuleTestSuiteResult` types, `runRuleTests()`, `validateRuleTestSuite()`, `formatRuleTestResults()` in rule.ts; 13 new tests
+- **Calibration pipeline integration** — `calibrate?: boolean | CalibrationOptions` on `EvaluationOptions`, wired `loadCalibrationProfile()` and `calibrateFindings()` into `evaluateWithTribunal()`; 5 new tests
+- **Finding diff between runs** — `FindingDiff` interface, `findingDiffKey()`, `diffFindings()` (classifies new/fixed/recurring), `formatFindingDiff()` in dedup.ts; 11 new tests
+- **`judges doctor` command** — Full diagnostic healthcheck: 7 checks (Node version, config file, judges loaded, plugins, feedback store, baseline file, presets), `runDoctorChecks()` runner, `formatDoctorReport()` formatter, `--json` CLI support; 12 new tests
+
+### Added — P3: Ecosystem & Integration
+- **Language coverage report** — `detectFileLanguage()`, `computeLanguageCoverage()`, `formatCoverageReport()` in coverage.ts; covers 16 languages with judge availability mapping; 11 new tests
+- **Finding snapshot & trend tracking** — `SnapshotStore` with versioned persistence, `recordSnapshot()` from findings, `computeTrend()` with improving/stable/regressing detection (10% threshold comparing recent vs early runs), `formatTrendReport()` with delta history; 12 new tests
+- **Rule hit metrics** — `computeRuleHitMetrics()` tracking active/silent rules, severity breakdown per rule, noisy-rule ranking with percentages, `findJudgeForRule()` prefix matching, `formatRuleHitReport()`; 11 new tests
+- **Project auto-detection for init wizard** — `detectLanguages()`, `detectFrameworksFromFiles()` (package.json + requirements.txt + file indicators), `classifyProjectType()` (9 project types), `detectCI()`, `detectMonorepo()`, `recommendPreset()` with confidence scoring, `formatProjectSummary()`, `formatRecommendation()`; 22 new tests
+
+### Tests
+- 1982 tests passing (0 failures)
+- 689 subsystem tests (up from 610), 45 new tests this release
+- New test sections: Finding Diff (§27), Doctor Diagnostics (§28), Language Coverage (§29), Finding Snapshot & Trend (§30), Rule Hit Metrics (§31), Project Auto-Detection (§32)
+
 ## [3.22.1] — 2026-03-04
 
 ### Fixed

package/dist/api.d.ts

@@ -8,11 +8,12 @@
  * const result = evaluateCode("const x = eval(input);", "typescript");
  * ```
  */
-export type { Severity, Verdict, Finding, Patch, LangFamily, JudgesConfig, RuleOverride, ProjectFile, ProjectVerdict, DiffVerdict, DependencyEntry, DependencyVerdict, JudgeEvaluation, TribunalVerdict, JudgeDefinition, EvaluationContextV2, EvidenceBundleV2, SpecializedFindingV2, TribunalVerdictV2, MustFixGateOptions, MustFixGateResult, AppBuilderWorkflowResult, PlainLanguageFinding, WorkflowTask, PolicyProfile, } from "./types.js";
+export type { Severity, Verdict, Finding, Patch, LangFamily, JudgesConfig, RuleOverride, ProjectFile, ProjectVerdict, DiffVerdict, DependencyEntry, DependencyVerdict, JudgeEvaluation, TribunalVerdict, JudgeDefinition, EvaluationContextV2, EvidenceBundleV2, SpecializedFindingV2, TribunalVerdictV2, MustFixGateOptions, MustFixGateResult, AppBuilderWorkflowResult, PlainLanguageFinding, WorkflowTask, PolicyProfile, SuppressionRecord, SuppressionResult, } from "./types.js";
 export { JudgesError, ConfigError, EvaluationError, ParseError } from "./errors.js";
-export { parseConfig, defaultConfig, mergeConfigs, discoverCascadingConfigs, loadCascadingConfig } from "./config.js";
+export { parseConfig, defaultConfig, mergeConfigs, discoverCascadingConfigs, loadCascadingConfig, loadPluginJudges, validatePluginSpecifiers, isValidJudgeDefinition, } from "./config.js";
 export { JUDGES, getJudge, getJudgeSummaries } from "./judges/index.js";
-export { evaluateWithJudge, evaluateWithTribunal, evaluateProject, evaluateDiff, analyzeDependencies, enrichWithPatches, crossEvaluatorDedup, applyInlineSuppressions, runAppBuilderWorkflow, formatVerdictAsMarkdown, formatEvaluationAsMarkdown, clearEvaluationCaches, } from "./evaluators/index.js";
+export { evaluateWithJudge, evaluateWithTribunal, evaluateProject, evaluateDiff, analyzeDependencies, enrichWithPatches, crossEvaluatorDedup, diffFindings, formatFindingDiff, applyInlineSuppressions, applyInlineSuppressionsWithAudit, runAppBuilderWorkflow, formatVerdictAsMarkdown, formatEvaluationAsMarkdown, clearEvaluationCaches, } from "./evaluators/index.js";
+export type { FindingDiff } from "./evaluators/index.js";
 export { evaluateCodeV2, evaluateProjectV2, getSupportedPolicyProfiles } from "./evaluators/v2.js";
 export { analyzeCrossFileTaint } from "./ast/cross-file-taint.js";
 export { buildSingleJudgeDeepReviewSection, buildTribunalDeepReviewSection, buildSimplifiedDeepReviewSection, isContentPolicyRefusal, DEEP_REVIEW_PROMPT_INTRO, DEEP_REVIEW_IDENTITY, } from "./tools/deep-review.js";
@@ -29,10 +30,12 @@ export { fingerprintCode, fingerprintToFindings } from "./fingerprint.js";
 export type { AiFingerprint, AiSignal } from "./fingerprint.js";
 export { buildCalibrationProfile, calibrateFindings, autoCalibrateFindings } from "./calibration.js";
 export type { CalibrationProfile } from "./calibration.js";
-export { loadFeedbackStore, saveFeedbackStore, computeFeedbackStats, getFpRateByRule } from "./commands/feedback.js";
-export type { FeedbackEntry, FeedbackStore, FeedbackVerdict, FeedbackStats } from "./commands/feedback.js";
+export { loadFeedbackStore, saveFeedbackStore, computeFeedbackStats, getFpRateByRule, mergeFeedbackStores, computeTeamFeedbackStats, formatTeamStatsOutput, } from "./commands/feedback.js";
+export type { FeedbackEntry, FeedbackStore, FeedbackVerdict, FeedbackStats, TeamFeedbackStats, RuleTeamStats, } from "./commands/feedback.js";
 export { loadFixHistory, saveFixHistory, computeFixStats, recordFixAccepted, recordFixRejected, getFixAcceptanceRate, getLowAcceptanceRules, } from "./fix-history.js";
 export type { FixOutcome, FixHistory, FixStats } from "./fix-history.js";
+export { testRule, runRuleTests, validateRuleTestSuite, formatRuleTestResults, deserializeRule, } from "./commands/rule.js";
+export type { RuleTestCase, RuleTestResult, RuleTestSuiteResult } from "./commands/rule.js";
 export { findingToDiagnostic, findingsToDiagnostics, findingsToCodeActions, formatForProblemMatcher, formatAsJsonRpc, } from "./formatters/diagnostics.js";
 export type { Diagnostic, DiagnosticSeverity, Position, Range, CodeAction, PublishDiagnosticsParams, } from "./formatters/diagnostics.js";
 export { compareCapabilities, formatComparisonReport, formatFullComparisonMatrix, TOOL_PROFILES, CAPABILITY_MATRIX, } from "./comparison.js";
@@ -40,6 +43,16 @@ export type { ToolProfile, ToolCapability, ComparisonResult } from "./comparison
 export { runBenchmarkSuite, benchmarkGate, formatBenchmarkReport } from "./commands/benchmark.js";
 export type { BenchmarkResult, BenchmarkGateOptions, BenchmarkGateResult } from "./commands/benchmark.js";
 export { getLanguagePack, listLanguagePacks, suggestPack, LANGUAGE_PACKS } from "./commands/language-packs.js";
+export { runDoctorChecks, formatDoctorReport, checkNodeVersion, checkConfigFile, checkJudgesLoaded, checkPlugins, checkFeedbackStore, checkBaselineFile, checkPresets, } from "./commands/doctor.js";
+export type { DoctorCheck, DoctorReport, CheckStatus } from "./commands/doctor.js";
+export { computeLanguageCoverage, formatCoverageReport, detectFileLanguage } from "./commands/coverage.js";
+export type { LanguageCoverageReport, LanguageCoverageEntry } from "./commands/coverage.js";
+export { createSnapshotStore, loadSnapshotStore, saveSnapshotStore, recordSnapshot, computeTrend, formatTrendReport, } from "./commands/snapshot.js";
+export type { FindingSnapshot, SnapshotStore, TrendPoint, TrendReport } from "./commands/snapshot.js";
+export { findJudgeForRule, computeRuleHitMetrics, formatRuleHitReport } from "./commands/rule-metrics.js";
+export type { RuleHitEntry, RuleHitMetrics } from "./commands/rule-metrics.js";
+export { detectLanguages, detectFrameworksFromFiles, classifyProjectType, detectCI, detectMonorepo, detectProjectSignals, recommendPreset, formatProjectSummary, formatRecommendation, } from "./commands/auto-detect.js";
+export type { ProjectSignals, ProjectType, PresetRecommendation } from "./commands/auto-detect.js";
 export { formatSmartOutput, formatSmartSingleJudge } from "./commands/smart-output.js";
 export type { SmartOutputOptions } from "./commands/smart-output.js";
 import type { EvaluationOptions } from "./evaluators/index.js";

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+{"version":3,"file":"api.d.ts","sourceRoot":"","sources":["../src/api.ts"],"names":[],"mappings":"AAAA;;;;;;;;;GASG;AAGH,YAAY,EACV,QAAQ,EACR,OAAO,EACP,OAAO,EACP,KAAK,EACL,UAAU,EACV,YAAY,EACZ,YAAY,EACZ,WAAW,EACX,cAAc,EACd,WAAW,EACX,eAAe,EACf,iBAAiB,EACjB,eAAe,EACf,eAAe,EACf,eAAe,EACf,mBAAmB,EACnB,gBAAgB,EAChB,oBAAoB,EACpB,iBAAiB,EACjB,kBAAkB,EAClB,iBAAiB,EACjB,wBAAwB,EACxB,oBAAoB,EACpB,YAAY,EACZ,aAAa,EACb,iBAAiB,EACjB,iBAAiB,GAClB,MAAM,YAAY,CAAC;AAGpB,OAAO,EAAE,WAAW,EAAE,WAAW,EAAE,eAAe,EAAE,UAAU,EAAE,MAAM,aAAa,CAAC;AAGpF,OAAO,EACL,WAAW,EACX,aAAa,EACb,YAAY,EACZ,wBAAwB,EACxB,mBAAmB,EACnB,gBAAgB,EAChB,wBAAwB,EACxB,sBAAsB,GACvB,MAAM,aAAa,CAAC;AAGrB,OAAO,EAAE,MAAM,EAAE,QAAQ,EAAE,iBAAiB,EAAE,MAAM,mBAAmB,CAAC;AAIxE,OAAO,EACL,iBAAiB,EACjB,oBAAoB,EACpB,eAAe,EACf,YAAY,EACZ,mBAAmB,EACnB,iBAAiB,EACjB,mBAAmB,EACnB,YAAY,EACZ,iBAAiB,EACjB,uBAAuB,EACvB,gCAAgC,EAChC,qBAAqB,EACrB,uBAAuB,EACvB,0BAA0B,EAC1B,qBAAqB,GACtB,MAAM,uBAAuB,CAAC;AAC/B,YAAY,EAAE,WAAW,EAAE,MAAM,uBAAuB,CAAC;AAGzD,OAAO,EAAE,cAAc,EAAE,iBAAiB,EAAE,0BAA0B,EAAE,MAAM,oBAAoB,CAAC;AAGnG,OAAO,EAAE,qBAAqB,EAAE,MAAM,2BAA2B,CAAC;AAGlE,OAAO,EACL,iCAAiC,EACjC,8BAA8B,EAC9B,gCAAgC,EAChC,sBAAsB,EACtB,wBAAwB,EACxB,oBAAoB,GACrB,MAAM,wBAAwB,CAAC;AAGhC,OAAO,EAAE,oBAAoB,EAAE,MAAM,oBAAoB,CAAC;AAG1D,OAAO,EAAE,QAAQ,EAAE,WAAW,EAAE,MAAM,YAAY,CAAC;AACnD,OAAO,EAAE,iBAAiB,EAAE,MAAM,yBAAyB,CAAC;AAG5D,OAAO,EAAE,eAAe,EAAE,iBAAiB,EAAE,cAAc,EAAE,gBAAgB,EAAE,MAAM,uBAAuB,CAAC;AAC7G,YAAY,EAAE,oBAAoB,EAAE,MAAM,uBAAuB,CAAC;AAClE,OAAO,EAAE,gBAAgB,EAAE,aAAa,EAAE,aAAa,EAAE,MAAM,qBAAqB,CAAC;AAGrF,OAAO,EAAE,MAAM,EAAE,MAAM,UAAU,CAAC;AAGlC,OAAO,EACL,cAAc,EACd,gBAAgB,EAChB,oBAAoB,EACpB,cAAc,EACd,eAAe,EACf,mBAAmB,EACnB,cAAc,EACd,aAAa,EACb,YAAY,GACb,MAAM,cAAc,CAAC;AACtB,YAAY,EAAE,UAAU,EAAE,YAAY,EAAE,kBAAkB,EAAE,MAAM,cAAc,CAAC;AAGjF,OAAO,EAAE,eAAe,EAAE,qBAAqB,EAAE,MAAM,kBAAkB,CAAC;AAC1E,YAAY,EAAE,aAAa,EAAE,QAAQ,EAAE,MAAM,kBAAkB,CAAC;AAGhE,OAAO,EAAE,uBAAuB,EAAE,iBAAiB,EAAE,qBAAqB,EAAE,MAAM,kBAAkB,CAAC;AACrG,YAAY,EAAE,kBAAkB,EAAE,MAAM,kBAAkB,CAAC;AAG3D,OAAO,EACL,iBAAiB,EACjB,iBAAiB,EACjB,oBAAoB,EACpB,eAAe,EACf,mBAAmB,EACnB,wBAAwB,EACxB,qBAAqB,GACtB,MAAM,wBAAwB,CAAC;AAChC,YAAY,EACV,aAAa,EACb,aAAa,EACb,eAAe,EACf,aAAa,EACb,iBAAiB,EACjB,aAAa,GACd,MAAM,wBAAwB,CAAC;AAGhC,OAAO,EACL,cAAc,EACd,cAAc,EACd,eAAe,EACf,iBAAiB,EACjB,iBAAiB,EACjB,oBAAoB,EACpB,qBAAqB,GACtB,MAAM,kBAAkB,CAAC;AAC1B,YAAY,EAAE,UAAU,EAAE,UAAU,EAAE,QAAQ,EAAE,MAAM,kBAAkB,CAAC;AAGzE,OAAO,EACL,QAAQ,EACR,YAAY,EACZ,qBAAqB,EACrB,qBAAqB,EACrB,eAAe,GAChB,MAAM,oBAAoB,CAAC;AAC5B,YAAY,EAAE,YAAY,EAAE,cAAc,EAAE,mBAAmB,EAAE,MAAM,oBAAoB,CAAC;AAG5F,OAAO,EACL,mBAAmB,EACnB,qBAAqB,EACrB,qBAAqB,EACrB,uBAAuB,EACvB,eAAe,GAChB,MAAM,6BAA6B,CAAC;AACrC,YAAY,EACV,UAAU,EACV,kBAAkB,EAClB,QAAQ,EACR,KAAK,EACL,UAAU,EACV,wBAAwB,GACzB,MAAM,6BAA6B,CAAC;AAGrC,OAAO,EACL,mBAAmB,EACnB,sBAAsB,EACtB,0BAA0B,EAC1B,aAAa,EACb,iBAAiB,GAClB,MAAM,iBAAiB,CAAC;AACzB,YAAY,EAAE,WAAW,EAAE,cAAc,EAAE,gBAAgB,EAAE,MAAM,iBAAiB,CAAC;AAGrF,OAAO,EAAE,iBAAiB,EAAE,aAAa,EAAE,qBAAqB,EAAE,MAAM,yBAAyB,CAAC;AAClG,YAAY,EAAE,eAAe,EAAE,oBAAoB,EAAE,mBAAmB,EAAE,MAAM,yBAAyB,CAAC;AAG1G,OAAO,EAAE,eAAe,EAAE,iBAAiB,EAAE,WAAW,EAAE,cAAc,EAAE,MAAM,8BAA8B,CAAC;AAE/G,OAAO,EACL,eAAe,EACf,kBAAkB,EAClB,gBAAgB,EAChB,eAAe,EACf,iBAAiB,EACjB,YAAY,EACZ,kBAAkB,EAClB,iBAAiB,EACjB,YAAY,GACb,MAAM,sBAAsB,CAAC;AAC9B,YAAY,EAAE,WAAW,EAAE,YAAY,EAAE,WAAW,EAAE,MAAM,sBAAsB,CAAC;AAGnF,OAAO,EAAE,uBAAuB,EAAE,oBAAoB,EAAE,kBAAkB,EAAE,MAAM,wBAAwB,CAAC;AAC3G,YAAY,EAAE,sBAAsB,EAAE,qBAAqB,EAAE,MAAM,wBAAwB,CAAC;AAG5F,OAAO,EACL,mBAAmB,EACnB,iBAAiB,EACjB,iBAAiB,EACjB,cAAc,EACd,YAAY,EACZ,iBAAiB,GAClB,MAAM,wBAAwB,CAAC;AAChC,YAAY,EAAE,eAAe,EAAE,aAAa,EAAE,UAAU,EAAE,WAAW,EAAE,MAAM,wBAAwB,CAAC;AAGtG,OAAO,EAAE,gBAAgB,EAAE,qBAAqB,EAAE,mBAAmB,EAAE,MAAM,4BAA4B,CAAC;AAC1G,YAAY,EAAE,YAAY,EAAE,cAAc,EAAE,MAAM,4BAA4B,CAAC;AAG/E,OAAO,EACL,eAAe,EACf,yBAAyB,EACzB,mBAAmB,EACnB,QAAQ,EACR,cAAc,EACd,oBAAoB,EACpB,eAAe,EACf,oBAAoB,EACpB,oBAAoB,GACrB,MAAM,2BAA2B,CAAC;AACnC,YAAY,EAAE,cAAc,EAAE,WAAW,EAAE,oBAAoB,EAAE,MAAM,2BAA2B,CAAC;AAEnG,OAAO,EAAE,iBAAiB,EAAE,sBAAsB,EAAE,MAAM,4BAA4B,CAAC;AACvF,YAAY,EAAE,kBAAkB,EAAE,MAAM,4BAA4B,CAAC;AAKrE,OAAO,KAAK,EAAE,iBAAiB,EAAE,MAAM,uBAAuB,CAAC;AAC/D,OAAO,KAAK,EAAE,eAAe,EAAE,eAAe,EAAE,MAAM,YAAY,CAAC;AAInE;;;;;;;GAOG;AACH,wBAAgB,YAAY,CAAC,IAAI,EAAE,MAAM,EAAE,QAAQ,EAAE,MAAM,EAAE,OAAO,CAAC,EAAE,iBAAiB,GAAG,eAAe,CAEzG;AAED;;;;;;;;GAQG;AACH,wBAAgB,uBAAuB,CACrC,OAAO,EAAE,MAAM,EACf,IAAI,EAAE,MAAM,EACZ,QAAQ,EAAE,MAAM,EAChB,OAAO,CAAC,EAAE,iBAAiB,GAC1B,eAAe,CAMjB;AAID,OAAO,EAAE,6BAA6B,EAAE,MAAM,uCAAuC,CAAC;AACtF,YAAY,EAAE,cAAc,EAAE,MAAM,uCAAuC,CAAC;AAI5E,MAAM,WAAW,SAAS;IACxB,qCAAqC;IACrC,IAAI,EAAE,MAAM,CAAC;IACb,0BAA0B;IAC1B,IAAI,EAAE,MAAM,CAAC;IACb,2BAA2B;IAC3B,QAAQ,EAAE,MAAM,CAAC;CAClB;AAED,MAAM,WAAW,oBAAoB;IACnC,mCAAmC;IACnC,IAAI,EAAE,MAAM,CAAC;IACb,qCAAqC;IACrC,OAAO,EAAE,eAAe,CAAC;IACzB,kCAAkC;IAClC,KAAK,EAAE,MAAM,CAAC;CACf;AAED;;;;;;;;;;GAUG;AACH,wBAAuB,mBAAmB,CACxC,KAAK,EAAE,SAAS,EAAE,EAClB,OAAO,CAAC,EAAE,iBAAiB,GAC1B,cAAc,CAAC,oBAAoB,CAAC,CAMtC;AAED;;;;;;;;GAQG;AACH,wBAAsB,kBAAkB,CACtC,KAAK,EAAE,SAAS,EAAE,EAClB,WAAW,SAAI,EACf,OAAO,CAAC,EAAE,iBAAiB,EAC3B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package/dist/api.js

@@ -11,11 +11,11 @@
 // ─── Errors ──────────────────────────────────────────────────────────────────
 export { JudgesError, ConfigError, EvaluationError, ParseError } from "./errors.js";
 // ─── Config ──────────────────────────────────────────────────────────────────
-export { parseConfig, defaultConfig, mergeConfigs, discoverCascadingConfigs, loadCascadingConfig } from "./config.js";
+export { parseConfig, defaultConfig, mergeConfigs, discoverCascadingConfigs, loadCascadingConfig, loadPluginJudges, validatePluginSpecifiers, isValidJudgeDefinition, } from "./config.js";
 // ─── Judge Registry ──────────────────────────────────────────────────────────
 export { JUDGES, getJudge, getJudgeSummaries } from "./judges/index.js";
 // ─── Core Evaluation Functions ───────────────────────────────────────────────
-export { evaluateWithJudge, evaluateWithTribunal, evaluateProject, evaluateDiff, analyzeDependencies, enrichWithPatches, crossEvaluatorDedup, applyInlineSuppressions, runAppBuilderWorkflow, formatVerdictAsMarkdown, formatEvaluationAsMarkdown, clearEvaluationCaches, } from "./evaluators/index.js";
+export { evaluateWithJudge, evaluateWithTribunal, evaluateProject, evaluateDiff, analyzeDependencies, enrichWithPatches, crossEvaluatorDedup, diffFindings, formatFindingDiff, applyInlineSuppressions, applyInlineSuppressionsWithAudit, runAppBuilderWorkflow, formatVerdictAsMarkdown, formatEvaluationAsMarkdown, clearEvaluationCaches, } from "./evaluators/index.js";
 // ─── V2 Policy-Aware API ────────────────────────────────────────────────────
 export { evaluateCodeV2, evaluateProjectV2, getSupportedPolicyProfiles } from "./evaluators/v2.js";
 // ─── Cross-File Taint Analysis ───────────────────────────────────────────────
@@ -39,9 +39,11 @@ export { fingerprintCode, fingerprintToFindings } from "./fingerprint.js";
 // ─── Confidence Calibration ─────────────────────────────────────────────────
 export { buildCalibrationProfile, calibrateFindings, autoCalibrateFindings } from "./calibration.js";
 // ─── Feedback ────────────────────────────────────────────────────────────────
-export { loadFeedbackStore, saveFeedbackStore, computeFeedbackStats, getFpRateByRule } from "./commands/feedback.js";
+export { loadFeedbackStore, saveFeedbackStore, computeFeedbackStats, getFpRateByRule, mergeFeedbackStores, computeTeamFeedbackStats, formatTeamStatsOutput, } from "./commands/feedback.js";
 // ─── Fix History / Learning ──────────────────────────────────────────────────
 export { loadFixHistory, saveFixHistory, computeFixStats, recordFixAccepted, recordFixRejected, getFixAcceptanceRate, getLowAcceptanceRules, } from "./fix-history.js";
+// ─── Custom Rule Testing ────────────────────────────────────────────────────
+export { testRule, runRuleTests, validateRuleTestSuite, formatRuleTestResults, deserializeRule, } from "./commands/rule.js";
 // ─── IDE Diagnostics ─────────────────────────────────────────────────────────
 export { findingToDiagnostic, findingsToDiagnostics, findingsToCodeActions, formatForProblemMatcher, formatAsJsonRpc, } from "./formatters/diagnostics.js";
 // ─── Comparison Benchmarks ───────────────────────────────────────────────────
@@ -50,6 +52,16 @@ export { compareCapabilities, formatComparisonReport, formatFullComparisonMatrix
 export { runBenchmarkSuite, benchmarkGate, formatBenchmarkReport } from "./commands/benchmark.js";
 // ─── Language Packs ──────────────────────────────────────────────────────────
 export { getLanguagePack, listLanguagePacks, suggestPack, LANGUAGE_PACKS } from "./commands/language-packs.js";
+// ─── Doctor Diagnostics ──────────────────────────────────────────────────
+export { runDoctorChecks, formatDoctorReport, checkNodeVersion, checkConfigFile, checkJudgesLoaded, checkPlugins, checkFeedbackStore, checkBaselineFile, checkPresets, } from "./commands/doctor.js";
+// ─── Language Coverage ──────────────────────────────────────────────────────
+export { computeLanguageCoverage, formatCoverageReport, detectFileLanguage } from "./commands/coverage.js";
+// ─── Finding Snapshots & Trends ─────────────────────────────────────────────
+export { createSnapshotStore, loadSnapshotStore, saveSnapshotStore, recordSnapshot, computeTrend, formatTrendReport, } from "./commands/snapshot.js";
+// ─── Rule Hit Metrics ───────────────────────────────────────────────────────
+export { findJudgeForRule, computeRuleHitMetrics, formatRuleHitReport } from "./commands/rule-metrics.js";
+// ─── Project Auto-Detection ─────────────────────────────────────────────────
+export { detectLanguages, detectFrameworksFromFiles, classifyProjectType, detectCI, detectMonorepo, detectProjectSignals, recommendPreset, formatProjectSummary, formatRecommendation, } from "./commands/auto-detect.js";
 // ─── Smart Output ────────────────────────────────────────────────────────────
 export { formatSmartOutput, formatSmartSingleJudge } from "./commands/smart-output.js";
 // ─── Convenience Aliases ─────────────────────────────────────────────────────

package/dist/api.js.map

@@ -1 +1 @@
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+{"version":3,"file":"api.js","sourceRoot":"","sources":["../src/api.ts"],"names":[],"mappings":"AAAA;;;;;;;;;GASG;AAiCH,gFAAgF;AAChF,OAAO,EAAE,WAAW,EAAE,WAAW,EAAE,eAAe,EAAE,UAAU,EAAE,MAAM,aAAa,CAAC;AAEpF,gFAAgF;AAChF,OAAO,EACL,WAAW,EACX,aAAa,EACb,YAAY,EACZ,wBAAwB,EACxB,mBAAmB,EACnB,gBAAgB,EAChB,wBAAwB,EACxB,sBAAsB,GACvB,MAAM,aAAa,CAAC;AAErB,gFAAgF;AAChF,OAAO,EAAE,MAAM,EAAE,QAAQ,EAAE,iBAAiB,EAAE,MAAM,mBAAmB,CAAC;AAExE,gFAAgF;AAEhF,OAAO,EACL,iBAAiB,EACjB,oBAAoB,EACpB,eAAe,EACf,YAAY,EACZ,mBAAmB,EACnB,iBAAiB,EACjB,mBAAmB,EACnB,YAAY,EACZ,iBAAiB,EACjB,uBAAuB,EACvB,gCAAgC,EAChC,qBAAqB,EACrB,uBAAuB,EACvB,0BAA0B,EAC1B,qBAAqB,GACtB,MAAM,uBAAuB,CAAC;AAG/B,+EAA+E;AAC/E,OAAO,EAAE,cAAc,EAAE,iBAAiB,EAAE,0BAA0B,EAAE,MAAM,oBAAoB,CAAC;AAEnG,gFAAgF;AAChF,OAAO,EAAE,qBAAqB,EAAE,MAAM,2BAA2B,CAAC;AAElE,gFAAgF;AAChF,OAAO,EACL,iCAAiC,EACjC,8BAA8B,EAC9B,gCAAgC,EAChC,sBAAsB,EACtB,wBAAwB,EACxB,oBAAoB,GACrB,MAAM,wBAAwB,CAAC;AAEhC,gFAAgF;AAChF,OAAO,EAAE,oBAAoB,EAAE,MAAM,oBAAoB,CAAC;AAE1D,gFAAgF;AAChF,OAAO,EAAE,QAAQ,EAAE,WAAW,EAAE,MAAM,YAAY,CAAC;AACnD,OAAO,EAAE,iBAAiB,EAAE,MAAM,yBAAyB,CAAC;AAE5D,gFAAgF;AAChF,OAAO,EAAE,eAAe,EAAE,iBAAiB,EAAE,cAAc,EAAE,gBAAgB,EAAE,MAAM,uBAAuB,CAAC;AAE7G,OAAO,EAAE,gBAAgB,EAAE,aAAa,EAAE,aAAa,EAAE,MAAM,qBAAqB,CAAC;AAErF,gFAAgF;AAChF,OAAO,EAAE,MAAM,EAAE,MAAM,UAAU,CAAC;AAElC,gFAAgF;AAChF,OAAO,EACL,cAAc,EACd,gBAAgB,EAChB,oBAAoB,EACpB,cAAc,EACd,eAAe,EACf,mBAAmB,EACnB,cAAc,EACd,aAAa,EACb,YAAY,GACb,MAAM,cAAc,CAAC;AAGtB,+EAA+E;AAC/E,OAAO,EAAE,eAAe,EAAE,qBAAqB,EAAE,MAAM,kBAAkB,CAAC;AAG1E,+EAA+E;AAC/E,OAAO,EAAE,uBAAuB,EAAE,iBAAiB,EAAE,qBAAqB,EAAE,MAAM,kBAAkB,CAAC;AAGrG,gFAAgF;AAChF,OAAO,EACL,iBAAiB,EACjB,iBAAiB,EACjB,oBAAoB,EACpB,eAAe,EACf,mBAAmB,EACnB,wBAAwB,EACxB,qBAAqB,GACtB,MAAM,wBAAwB,CAAC;AAUhC,gFAAgF;AAChF,OAAO,EACL,cAAc,EACd,cAAc,EACd,eAAe,EACf,iBAAiB,EACjB,iBAAiB,EACjB,oBAAoB,EACpB,qBAAqB,GACtB,MAAM,kBAAkB,CAAC;AAG1B,+EAA+E;AAC/E,OAAO,EACL,QAAQ,EACR,YAAY,EACZ,qBAAqB,EACrB,qBAAqB,EACrB,eAAe,GAChB,MAAM,oBAAoB,CAAC;AAG5B,gFAAgF;AAChF,OAAO,EACL,mBAAmB,EACnB,qBAAqB,EACrB,qBAAqB,EACrB,uBAAuB,EACvB,eAAe,GAChB,MAAM,6BAA6B,CAAC;AAUrC,gFAAgF;AAChF,OAAO,EACL,mBAAmB,EACnB,sBAAsB,EACtB,0BAA0B,EAC1B,aAAa,EACb,iBAAiB,GAClB,MAAM,iBAAiB,CAAC;AAGzB,gFAAgF;AAChF,OAAO,EAAE,iBAAiB,EAAE,aAAa,EAAE,qBAAqB,EAAE,MAAM,yBAAyB,CAAC;AAGlG,gFAAgF;AAChF,OAAO,EAAE,eAAe,EAAE,iBAAiB,EAAE,WAAW,EAAE,cAAc,EAAE,MAAM,8BAA8B,CAAC;AAC/G,4EAA4E;AAC5E,OAAO,EACL,eAAe,EACf,kBAAkB,EAClB,gBAAgB,EAChB,eAAe,EACf,iBAAiB,EACjB,YAAY,EACZ,kBAAkB,EAClB,iBAAiB,EACjB,YAAY,GACb,MAAM,sBAAsB,CAAC;AAG9B,+EAA+E;AAC/E,OAAO,EAAE,uBAAuB,EAAE,oBAAoB,EAAE,kBAAkB,EAAE,MAAM,wBAAwB,CAAC;AAG3G,+EAA+E;AAC/E,OAAO,EACL,mBAAmB,EACnB,iBAAiB,EACjB,iBAAiB,EACjB,cAAc,EACd,YAAY,EACZ,iBAAiB,GAClB,MAAM,wBAAwB,CAAC;AAGhC,+EAA+E;AAC/E,OAAO,EAAE,gBAAgB,EAAE,qBAAqB,EAAE,mBAAmB,EAAE,MAAM,4BAA4B,CAAC;AAG1G,+EAA+E;AAC/E,OAAO,EACL,eAAe,EACf,yBAAyB,EACzB,mBAAmB,EACnB,QAAQ,EACR,cAAc,EACd,oBAAoB,EACpB,eAAe,EACf,oBAAoB,EACpB,oBAAoB,GACrB,MAAM,2BAA2B,CAAC;AAEnC,gFAAgF;AAChF,OAAO,EAAE,iBAAiB,EAAE,sBAAsB,EAAE,MAAM,4BAA4B,CAAC;AAGvF,gFAAgF;AAEhF,OAAO,EAAE,oBAAoB,EAAE,iBAAiB,EAAE,MAAM,uBAAuB,CAAC;AAGhF,OAAO,EAAE,QAAQ,EAAE,MAAM,mBAAmB,CAAC;AAC7C,OAAO,EAAE,eAAe,EAAE,MAAM,aAAa,CAAC;AAE9C;;;;;;;GAOG;AACH,MAAM,UAAU,YAAY,CAAC,IAAY,EAAE,QAAgB,EAAE,OAA2B;IACtF,OAAO,oBAAoB,CAAC,IAAI,EAAE,QAAQ,EAAE,SAAS,EAAE,OAAO,CAAC,CAAC;AAClE,CAAC;AAED;;;;;;;;GAQG;AACH,MAAM,UAAU,uBAAuB,CACrC,OAAe,EACf,IAAY,EACZ,QAAgB,EAChB,OAA2B;IAE3B,MAAM,KAAK,GAAG,QAAQ,CAAC,OAAO,CAAC,CAAC;IAChC,IAAI,CAAC,KAAK,EAAE,CAAC;QACX,MAAM,IAAI,eAAe,CAAC,mBAAmB,OAAO,GAAG,EAAE,OAAO,CAAC,CAAC;IACpE,CAAC;IACD,OAAO,iBAAiB,CAAC,KAAK,EAAE,IAAI,EAAE,QAAQ,EAAE,SAAS,EAAE,OAAO,CAAC,CAAC;AACtE,CAAC;AAED,gFAAgF;AAEhF,OAAO,EAAE,6BAA6B,EAAE,MAAM,uCAAuC,CAAC;AAuBtF;;;;;;;;;;GAUG;AACH,MAAM,CAAC,KAAK,SAAS,CAAC,CAAC,mBAAmB,CACxC,KAAkB,EAClB,OAA2B;IAE3B,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,KAAK,CAAC,MAAM,EAAE,CAAC,EAAE,EAAE,CAAC;QACtC,MAAM,IAAI,GAAG,KAAK,CAAC,CAAC,CAAC,CAAC;QACtB,MAAM,OAAO,GAAG,oBAAoB,CAAC,IAAI,CAAC,IAAI,EAAE,IAAI,CAAC,QAAQ,EAAE,SAAS,EAAE,OAAO,CAAC,CAAC;QACnF,MAAM,EAAE,IAAI,EAAE,IAAI,CAAC,IAAI,EAAE,OAAO,EAAE,KAAK,EAAE,CAAC,EAAE,CAAC;IAC/C,CAAC;AACH,CAAC;AAED;;;;;;;;GAQG;AACH,MAAM,CAAC,KAAK,UAAU,kBAAkB,CACtC,KAAkB,EAClB,WAAW,GAAG,CAAC,EACf,OAA2B,EAC3B,UAAuD;IAEvD,MAAM,OAAO,GAA2B,IAAI,KAAK,CAAC,KAAK,CAAC,MAAM,CAAC,CAAC;IAChE,IAAI,SAAS,GAAG,CAAC,CAAC;IAClB,IAAI,SAAS,GAAG,CAAC,CAAC;IAElB,KAAK,UAAU,MAAM;QACnB,OAAO,SAAS,GAAG,KAAK,CAAC,MAAM,EAAE,CAAC;YAChC,MAAM,CAAC,GAAG,SAAS,EAAE,CAAC;YACtB,MAAM,IAAI,GAAG,KAAK,CAAC,CAAC,CAAC,CAAC;YACtB,MAAM,OAAO,GAAG,oBAAoB,CAAC,IAAI,CAAC,IAAI,EAAE,IAAI,CAAC,QAAQ,EAAE,SAAS,EAAE,OAAO,CAAC,CAAC;YACnF,OAAO,CAAC,CAAC,CAAC,GAAG,EAAE,IAAI,EAAE,IAAI,CAAC,IAAI,EAAE,OAAO,EAAE,KAAK,EAAE,CAAC,EAAE,CAAC;YACpD,SAAS,EAAE,CAAC;YACZ,UAAU,EAAE,CAAC,SAAS,EAAE,KAAK,CAAC,MAAM,CAAC,CAAC;QACxC,CAAC;IACH,CAAC;IAED,MAAM,OAAO,GAAG,KAAK,CAAC,IAAI,CAAC,EAAE,MAAM,EAAE,IAAI,CAAC,GAAG,CAAC,WAAW,EAAE,KAAK,CAAC,MAAM,CAAC,EAAE,EAAE,GAAG,EAAE,CAAC,MAAM,EAAE,CAAC,CAAC;IAC5F,MAAM,OAAO,CAAC,GAAG,CAAC,OAAO,CAAC,CAAC;IAC3B,OAAO,OAAO,CAAC;AACjB,CAAC"}

package/dist/ast/structural-parser.js

@@ -474,10 +474,35 @@ function detectWeakTypes(lines, language) {
     const pattern = patterns[language];
     if (!pattern)
         return weakLines;
+    // Python: track `if TYPE_CHECKING:` blocks so that imports guarded by
+    // TYPE_CHECKING (used for static analysis only) are not flagged.
+    let inTypeCheckingBlock = false;
+    let typeCheckingIndent = -1;
     for (let i = 0; i < lines.length; i++) {
         const trimmed = lines[i].trim();
         if (trimmed.startsWith("//") || trimmed.startsWith("#") || trimmed.startsWith("/*"))
             continue;
+        if (language === "python") {
+            // Skip TYPE_CHECKING imports and lines referencing TYPE_CHECKING
+            if (/\bTYPE_CHECKING\b/.test(trimmed)) {
+                // Detect start of `if TYPE_CHECKING:` block
+                if (/^if\s+TYPE_CHECKING\s*:/.test(trimmed)) {
+                    inTypeCheckingBlock = true;
+                    typeCheckingIndent = (lines[i].match(/^(\s*)/)?.[1] ?? "").length;
+                }
+                continue;
+            }
+            // Skip lines inside an `if TYPE_CHECKING:` block
+            if (inTypeCheckingBlock) {
+                const currentIndent = (lines[i].match(/^(\s*)/)?.[1] ?? "").length;
+                if (trimmed.length > 0 && currentIndent <= typeCheckingIndent) {
+                    inTypeCheckingBlock = false;
+                }
+                else {
+                    continue;
+                }
+            }
+        }
         if (pattern.test(lines[i])) {
             weakLines.push(i + 1);
         }

package/dist/ast/structural-parser.js.map

@@ -1 +1 @@
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package/dist/cli.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"cli.d.ts","sourceRoot":"","sources":["../src/cli.ts"],"names":[],"mappings":";AAEA;;;;;;;;;;;;;;;;;;;GAmBG;AAqWH;;;GAGG;AACH,wBAAgB,WAAW,CAAC,OAAO,EAAE,MAAM,GAAG,MAAM,CAcnD;AAED,wBAAgB,WAAW,CAAC,QAAQ,EAAE,MAAM,EAAE,QAAQ,EAAE,MAAM,EAAE,GAAG,OAAO,CAQzE;AAiBD,UAAU,cAAc;IACtB,OAAO,CAAC,EAAE,MAAM,EAAE,CAAC;IACnB,OAAO,CAAC,EAAE,MAAM,EAAE,CAAC;IACnB,QAAQ,CAAC,EAAE,MAAM,CAAC;CACnB;AAED,wBAAgB,YAAY,CAAC,MAAM,EAAE,MAAM,EAAE,OAAO,GAAE,cAAmB,GAAG,MAAM,EAAE,CAiBnF;AA+LD,wBAAsB,MAAM,CAAC,IAAI,EAAE,MAAM,EAAE,GAAG,OAAO,CAAC,IAAI,CAAC,CAma1D"}
+{"version":3,"file":"cli.d.ts","sourceRoot":"","sources":["../src/cli.ts"],"names":[],"mappings":";AAEA;;;;;;;;;;;;;;;;;;;GAmBG;AAuWH;;;GAGG;AACH,wBAAgB,WAAW,CAAC,OAAO,EAAE,MAAM,GAAG,MAAM,CAcnD;AAED,wBAAgB,WAAW,CAAC,QAAQ,EAAE,MAAM,EAAE,QAAQ,EAAE,MAAM,EAAE,GAAG,OAAO,CAQzE;AAiBD,UAAU,cAAc;IACtB,OAAO,CAAC,EAAE,MAAM,EAAE,CAAC;IACnB,OAAO,CAAC,EAAE,MAAM,EAAE,CAAC;IACnB,QAAQ,CAAC,EAAE,MAAM,CAAC;CACnB;AAED,wBAAgB,YAAY,CAAC,MAAM,EAAE,MAAM,EAAE,OAAO,GAAE,cAAmB,GAAG,MAAM,EAAE,CAiBnF;AA+LD,wBAAsB,MAAM,CAAC,IAAI,EAAE,MAAM,EAAE,GAAG,OAAO,CAAC,IAAI,CAAC,CA2a1D"}

package/dist/cli.js

@@ -32,7 +32,7 @@ import { runReport } from "./commands/report.js";
 import { runHook } from "./commands/hook.js";
 import { runDiff } from "./commands/diff.js";
 import { runDeps } from "./commands/deps.js";
-import { runBaseline } from "./commands/baseline.js";
+import { runBaseline, loadBaselineData, isBaselined } from "./commands/baseline.js";
 import { runCompletions } from "./commands/completions.js";
 import { runDocs } from "./commands/docs.js";
 import { generateGitLabCi, generateAzurePipelines, generateBitbucketPipelines } from "./commands/ci-templates.js";
@@ -44,6 +44,7 @@ import { runBenchmark } from "./commands/benchmark.js";
 import { runRule } from "./commands/rule.js";
 import { runPack } from "./commands/language-packs.js";
 import { runConfig } from "./commands/config-share.js";
+import { runDoctor } from "./commands/doctor.js";
 import { formatComparisonReport, formatFullComparisonMatrix, TOOL_PROFILES } from "./comparison.js";
 // ─── Language Detection from Extension ──────────────────────────────────────
 const EXT_TO_LANG = {
@@ -207,6 +208,7 @@ USAGE:
   judges hook install                 Install pre-commit git hook
   judges diff                         Evaluate only changed lines from a diff
   judges deps [dir]                   Analyze dependencies for supply-chain risks
+  judges doctor                       Run diagnostic healthcheck
   judges baseline create <file>       Create a findings baseline
   judges ci-templates <provider>      Generate CI pipeline template
   judges completions <shell>          Generate shell completions
@@ -612,6 +614,11 @@ export async function runCli(argv) {
         runDeps(argv);
         return;
     }
+    // ─── Doctor Command ──────────────────────────────────────────────────
+    if (args.command === "doctor") {
+        runDoctor(argv);
+        return;
+    }
     // ─── Baseline Command ────────────────────────────────────────────────
     if (args.command === "baseline") {
         runBaseline(argv);
@@ -685,9 +692,9 @@ export async function runCli(argv) {
         // Load config from file or preset
         const evalConfig = loadEvalConfig(args);
         // Load baseline if specified (from CLI flag — config doesn't carry baseline)
-        let baselineFindings;
+        let loadedBaseline;
         if (args.baseline) {
-            baselineFindings = loadBaseline(args.baseline);
+            loadedBaseline = loadBaselineData(args.baseline);
         }
         // Build evaluation options from config
         const evalOptions = evalConfig ? { config: evalConfig } : undefined;
@@ -725,11 +732,11 @@ export async function runCli(argv) {
                 const fileLang = args.language || detectLanguage(filePath) || "typescript";
                 const verdict = evaluateWithTribunal(fileCode, fileLang, undefined, evalOptions);
                 // Apply baseline suppression
-                if (baselineFindings) {
+                if (loadedBaseline) {
                     for (const evaluation of verdict.evaluations) {
-                        evaluation.findings = evaluation.findings.filter((f) => !baselineFindings.has(baselineKey(f)));
+                        evaluation.findings = evaluation.findings.filter((f) => !isBaselined(f, loadedBaseline, fileCode, relPath));
                     }
-                    verdict.findings = verdict.findings.filter((f) => !baselineFindings.has(baselineKey(f)));
+                    verdict.findings = verdict.findings.filter((f) => !isBaselined(f, loadedBaseline, fileCode, relPath));
                 }
                 const fileFindings = verdict.evaluations.reduce((s, e) => s + e.findings.length, 0);
                 totalFindings += fileFindings;
@@ -794,8 +801,8 @@ export async function runCli(argv) {
             }
             const evaluation = evaluateWithJudge(judge, code, language);
             // Apply baseline suppression
-            if (baselineFindings) {
-                evaluation.findings = evaluation.findings.filter((f) => !baselineFindings.has(baselineKey(f)));
+            if (loadedBaseline) {
+                evaluation.findings = evaluation.findings.filter((f) => !isBaselined(f, loadedBaseline, code));
             }
             // Apply min-severity filter from config
             if (evalConfig?.minSeverity) {
@@ -866,11 +873,11 @@ export async function runCli(argv) {
             // Full tribunal mode
             const verdict = evaluateWithTribunal(code, language, undefined, evalOptions);
             // Apply baseline suppression
-            if (baselineFindings) {
+            if (loadedBaseline) {
                 for (const evaluation of verdict.evaluations) {
-                    evaluation.findings = evaluation.findings.filter((f) => !baselineFindings.has(baselineKey(f)));
+                    evaluation.findings = evaluation.findings.filter((f) => !isBaselined(f, loadedBaseline, code));
                 }
-                verdict.findings = verdict.findings.filter((f) => !baselineFindings.has(baselineKey(f)));
+                verdict.findings = verdict.findings.filter((f) => !isBaselined(f, loadedBaseline, code));
             }
             // Apply min-severity filter from config
             if (evalConfig?.minSeverity) {
@@ -940,30 +947,8 @@ export async function runCli(argv) {
     process.exit(1);
 }
 // ─── Baseline Support ───────────────────────────────────────────────────────
-function baselineKey(f) {
-    const line = f.lineNumbers?.[0] ?? 0;
-    return `${f.ruleId}::${line}::${f.title}`;
-}
-function loadBaseline(baselinePath) {
-    const abs = resolve(baselinePath);
-    if (!existsSync(abs)) {
-        return new Set();
-    }
-    try {
-        const data = JSON.parse(readFileSync(abs, "utf-8"));
-        const keys = new Set();
-        if (Array.isArray(data.findings)) {
-            for (const f of data.findings) {
-                keys.add(baselineKey(f));
-            }
-        }
-        return keys;
-    }
-    catch {
-        console.error(`Warning: Could not parse baseline file: ${baselinePath}`);
-        return new Set();
-    }
-}
+// Baseline loading and matching is now handled by src/commands/baseline.ts
+// Exports: loadBaselineData, isBaselined, LoadedBaseline
 // ─── Summary Line Output ───────────────────────────────────────────────────
 function printSummaryLine(verdict, score, findings) {
     const icon = verdict === "pass" ? "✅" : verdict === "warning" ? "⚠️" : "❌";
@@ -972,7 +957,7 @@ function printSummaryLine(verdict, score, findings) {
 // ─── Config / Preset Loader ────────────────────────────────────────────────
 function loadEvalConfig(args) {
     let config;
-    // 1. Load from preset (supports comma-separated composition: "security-only,performance")
+    // 1. Load from CLI --preset (supports comma-separated composition: "security-only,performance")
     if (args.preset) {
         const presetNames = args.preset.split(",").map((n) => n.trim());
         if (presetNames.length === 1) {
@@ -1024,6 +1009,39 @@ function loadEvalConfig(args) {
             }
         }
     }
+    // 4. Apply config.preset if no CLI --preset was given
+    if (config?.preset && !args.preset) {
+        const presetNames = config.preset.split(",").map((n) => n.trim());
+        let presetConfig;
+        if (presetNames.length === 1) {
+            const preset = getPreset(presetNames[0]);
+            if (preset)
+                presetConfig = { ...preset.config };
+        }
+        else {
+            const composed = composePresets(presetNames);
+            if (composed)
+                presetConfig = { ...composed.config };
+        }
+        if (presetConfig) {
+            // Preset is the base; config file properties override it
+            const { preset: _p, ...rest } = config;
+            config = { ...presetConfig, ...rest };
+        }
+    }
+    // 5. Apply config-based defaults to CLI args (CLI flags always win)
+    if (config) {
+        if (config.failOnFindings && !args.failOnFindings) {
+            args.failOnFindings = true;
+        }
+        if (config.baseline && !args.baseline) {
+            args.baseline = config.baseline;
+        }
+        if (config.format && args.format === "text") {
+            // Only apply config format if CLI didn't explicitly set one
+            args.format = config.format;
+        }
+    }
     return config;
 }
 // ─── Severity Filter ────────────────────────────────────────────────────────