@skill-map/cli 0.28.0 → 0.29.0

package/dist/index.js

@@ -93,14 +93,14 @@ var Registry = class {
 };
 
 // kernel/orchestrator/index.ts
-import { existsSync as existsSync9, statSync as statSync2 } from "fs";
+import { existsSync as existsSync10, statSync as statSync4 } from "fs";
 import { Tiktoken as Tiktoken2 } from "js-tiktoken/lite";
 import cl100k_base from "js-tiktoken/ranks/cl100k_base";
 
 // package.json
 var package_default = {
   name: "@skill-map/cli",
-  version: "0.28.0",
+  version: "0.29.0",
   description: "skill-map reference implementation \u2014 kernel + CLI + adapters.",
   license: "MIT",
   type: "module",
@@ -153,16 +153,19 @@ var package_default = {
     "lint:fix": "eslint . --fix",
     reference: "node scripts/build-reference.js",
     "reference:check": "node scripts/build-reference.js --check",
+    "build-built-ins": "node ../scripts/generate-built-ins.js",
+    "built-ins:check": "node ../scripts/generate-built-ins.js --check",
+    prebuild: "pnpm build-built-ins",
     validate: "pnpm validate:compile && pnpm validate:test",
-    "validate:compile": "pnpm typecheck && pnpm lint && pnpm build && pnpm reference:check",
+    "validate:compile": "pnpm typecheck && pnpm lint && pnpm build && pnpm reference:check && pnpm built-ins:check",
     "validate:test": "pnpm test:ci",
     pretest: "tsup",
     "pretest:coverage": "tsup",
     "pretest:coverage:html": "tsup",
-    test: "tsc --noEmit && node --import tsx --test --test-reporter=spec 'test/**/*.test.ts' 'built-in-plugins/**/*.test.ts' 'kernel/**/*.test.ts' 'server/**/*.test.ts'",
-    "test:ci": "node --import tsx --test 'test/**/*.test.ts' 'built-in-plugins/**/*.test.ts' 'kernel/**/*.test.ts' 'server/**/*.test.ts'",
-    "test:coverage": "tsc --noEmit && SKILL_MAP_SKIP_BENCHMARK=1 node --experimental-default-config-file --import tsx --test --experimental-test-coverage 'test/**/*.test.ts' 'built-in-plugins/**/*.test.ts' 'kernel/**/*.test.ts' 'server/**/*.test.ts'",
-    "test:coverage:html": "tsc --noEmit && SKILL_MAP_SKIP_BENCHMARK=1 c8 node --import tsx --test 'test/**/*.test.ts' 'built-in-plugins/**/*.test.ts' 'kernel/**/*.test.ts' 'server/**/*.test.ts'",
+    test: "tsc --noEmit && node --import tsx --test --test-reporter=spec '__tests__/**/*.spec.ts' 'kernel/**/__tests__/**/*.spec.ts' 'cli/**/__tests__/**/*.spec.ts' 'server/**/__tests__/**/*.spec.ts' 'plugins/**/__tests__/**/*.spec.ts' 'core/**/__tests__/**/*.spec.ts' 'conformance/**/__tests__/**/*.spec.ts'",
+    "test:ci": "node --import tsx --test '__tests__/**/*.spec.ts' 'kernel/**/__tests__/**/*.spec.ts' 'cli/**/__tests__/**/*.spec.ts' 'server/**/__tests__/**/*.spec.ts' 'plugins/**/__tests__/**/*.spec.ts' 'core/**/__tests__/**/*.spec.ts' 'conformance/**/__tests__/**/*.spec.ts'",
+    "test:coverage": "tsc --noEmit && SKILL_MAP_SKIP_BENCHMARK=1 node --experimental-default-config-file --import tsx --test --experimental-test-coverage '__tests__/**/*.spec.ts' 'kernel/**/__tests__/**/*.spec.ts' 'cli/**/__tests__/**/*.spec.ts' 'server/**/__tests__/**/*.spec.ts' 'plugins/**/__tests__/**/*.spec.ts' 'core/**/__tests__/**/*.spec.ts' 'conformance/**/__tests__/**/*.spec.ts'",
+    "test:coverage:html": "tsc --noEmit && SKILL_MAP_SKIP_BENCHMARK=1 c8 node --import tsx --test '__tests__/**/*.spec.ts' 'kernel/**/__tests__/**/*.spec.ts' 'cli/**/__tests__/**/*.spec.ts' 'server/**/__tests__/**/*.spec.ts' 'plugins/**/__tests__/**/*.spec.ts' 'core/**/__tests__/**/*.spec.ts' 'conformance/**/__tests__/**/*.spec.ts'",
     clean: "rm -rf dist coverage"
   },
   dependencies: {
@@ -220,8 +223,8 @@ var InMemoryProgressEmitter = class {
 
 // kernel/adapters/plugin-loader/index.ts
 import { createRequire } from "module";
-import { existsSync, readFileSync as readFileSync2, readdirSync } from "fs";
-import { join, resolve as resolve3 } from "path";
+import { existsSync as existsSync2, readFileSync as readFileSync3, readdirSync as readdirSync2, statSync as statSync2 } from "fs";
+import { join as join2, resolve as resolve3 } from "path";
 import { pathToFileURL } from "url";
 import semver from "semver";
 
@@ -229,6 +232,9 @@ import semver from "semver";
 import { isAbsolute, relative, resolve } from "path";
 
 // kernel/adapters/plugin-loader/validation.ts
+import * as nodeFs from "fs";
+import { existsSync } from "fs";
+import { dirname, join } from "path";
 import { Ajv2020 } from "ajv/dist/2020.js";
 
 // kernel/util/ajv-interop.ts
@@ -265,7 +271,7 @@ var KNOWN_KINDS_LIST = [...KNOWN_KINDS].join(" / ");
 var HOOKABLE_TRIGGERS_LIST = HOOK_TRIGGERS.join(", ");
 
 // kernel/adapters/plugin-loader/storage-schemas.ts
-import { readFileSync } from "fs";
+import { readFileSync as readFileSync2 } from "fs";
 import { resolve as resolve2 } from "path";
 import { Ajv2020 as Ajv20202 } from "ajv/dist/2020.js";
 
@@ -326,7 +332,7 @@ function makePluginStore(opts) {
     if (!opts.persistKv) return void 0;
     const schema = storageSchemas?.[KV_SCHEMA_KEY];
     return makeKvStoreWrapper({
-      pluginId: manifest.id,
+      pluginId: opts.plugin.id,
       schema,
       persist: opts.persistKv
     });
@@ -334,7 +340,7 @@ function makePluginStore(opts) {
   if (manifest.storage.mode === "dedicated") {
     if (!opts.persistDedicated) return void 0;
     return makeDedicatedStoreWrapper({
-      pluginId: manifest.id,
+      pluginId: opts.plugin.id,
       schemas: storageSchemas,
       persist: opts.persistDedicated
     });
@@ -351,13 +357,13 @@ function installedSpecVersion() {
   const require2 = createRequire(import.meta.url);
   const indexPath = require2.resolve("@skill-map/spec/index.json");
   const pkgPath = resolve3(indexPath, "..", "package.json");
-  const pkg = JSON.parse(readFileSync2(pkgPath, "utf8"));
+  const pkg = JSON.parse(readFileSync3(pkgPath, "utf8"));
   return pkg.version;
 }
 
 // kernel/adapters/schema-validators.ts
-import { readFileSync as readFileSync3 } from "fs";
-import { dirname, resolve as resolve4 } from "path";
+import { readFileSync as readFileSync4 } from "fs";
+import { dirname as dirname2, resolve as resolve4 } from "path";
 import { createRequire as createRequire2 } from "module";
 import { Ajv2020 as Ajv20203 } from "ajv/dist/2020.js";
 
@@ -395,6 +401,7 @@ var SCHEMA_FILES = {
   "conformance-case": "schemas/conformance-case.schema.json",
   "history-stats": "schemas/history-stats.schema.json",
   "extension-provider": "schemas/extensions/provider.schema.json",
+  "extension-provider-kind": "schemas/extensions/provider-kind.schema.json",
   "extension-extractor": "schemas/extensions/extractor.schema.json",
   "extension-analyzer": "schemas/extensions/analyzer.schema.json",
   "extension-action": "schemas/extensions/action.schema.json",
@@ -426,13 +433,13 @@ function buildSchemaValidators() {
   for (const rel of SUPPORTING_SCHEMAS) {
     const file = resolve4(specRoot, rel);
     if (!existsSyncSafe(file)) continue;
-    const schema = JSON.parse(readFileSync3(file, "utf8"));
+    const schema = JSON.parse(readFileSync4(file, "utf8"));
     ajv.addSchema(schema);
   }
   const validators = /* @__PURE__ */ new Map();
   for (const [name, rel] of Object.entries(SCHEMA_FILES)) {
     const file = resolve4(specRoot, rel);
-    const schema = JSON.parse(readFileSync3(file, "utf8"));
+    const schema = JSON.parse(readFileSync4(file, "utf8"));
     const byId = typeof schema.$id === "string" ? ajv.getSchema(schema.$id) : void 0;
     validators.set(name, byId ?? ajv.compile(schema));
   }
@@ -504,7 +511,7 @@ function buildProviderFrontmatterValidator(providers) {
   });
   applyAjvFormats(ajv);
   const baseFile = resolve4(specRoot, "schemas/frontmatter/base.schema.json");
-  const baseSchema = JSON.parse(readFileSync3(baseFile, "utf8"));
+  const baseSchema = JSON.parse(readFileSync4(baseFile, "utf8"));
   ajv.addSchema(baseSchema);
   registerProviderAuxiliarySchemas(ajv, providers);
   const compiled = /* @__PURE__ */ new Map();
@@ -545,7 +552,7 @@ function resolveSpecRoot() {
   const require2 = createRequire2(import.meta.url);
   try {
     const indexPath = require2.resolve("@skill-map/spec/index.json");
-    return dirname(indexPath);
+    return dirname2(indexPath);
   } catch {
     throw new Error(
       "@skill-map/spec not resolvable: ensure the workspace is linked or the package is installed."
@@ -554,7 +561,7 @@ function resolveSpecRoot() {
 }
 function existsSyncSafe(path) {
   try {
-    readFileSync3(path, "utf8");
+    readFileSync4(path, "utf8");
     return true;
   } catch {
     return false;
@@ -607,14 +614,6 @@ function makeHookDispatcher(hooks, emitter) {
   }
   const byTrigger = /* @__PURE__ */ new Map();
   for (const hook of hooks) {
-    if (hook.mode === "probabilistic") {
-      const qualifiedId = qualifiedExtensionId(hook.pluginId, hook.id);
-      log.warn(
-        `Probabilistic hook ${qualifiedId} deferred to job subsystem (future job subsystem). The hook is registered but will not dispatch in-scan.`,
-        { hookId: qualifiedId, mode: "probabilistic" }
-      );
-      continue;
-    }
     for (const trig of hook.triggers) {
       const bucket = byTrigger.get(trig);
       if (bucket) bucket.push(hook);
@@ -792,7 +791,7 @@ async function runExtractorsForNode(opts) {
 }
 function readDeclaredContributions(extension) {
   const out = /* @__PURE__ */ new Map();
-  const raw = extension.viewContributions;
+  const raw = extension.ui;
   if (typeof raw !== "object" || raw === null) return out;
   for (const [id, value] of Object.entries(raw)) {
     if (typeof value !== "object" || value === null) continue;
@@ -813,11 +812,13 @@ function emitExtensionError(emitter, qualifiedId, nodePath, data) {
   );
 }
 function buildExtractorContext(extractor, node, body, frontmatter, emitLink, enrichNode, emitContribution, store) {
-  const scope = extractor.scope;
+  const scope = extractor.scope ?? "both";
+  const settings = extractor.resolvedSettings ?? {};
   return {
     node,
     body: scope === "frontmatter" ? "" : body,
     frontmatter: scope === "body" ? {} : frontmatter,
+    settings,
     emitLink,
     enrichNode,
     emitContribution,
@@ -825,25 +826,26 @@ function buildExtractorContext(extractor, node, body, frontmatter, emitLink, enr
   };
 }
 function validateLink(extractor, link, emitter) {
-  if (!extractor.emitsLinkKinds.includes(link.kind)) {
+  const knownKinds = ["invokes", "references", "mentions", "supersedes"];
+  if (!knownKinds.includes(link.kind)) {
     const qualifiedId = `${extractor.pluginId}/${extractor.id}`;
     emitter.emit(
       makeEvent("extension.error", {
         kind: "link-kind-not-declared",
         extensionId: qualifiedId,
         linkKind: link.kind,
-        declaredKinds: extractor.emitsLinkKinds,
+        declaredKinds: knownKinds,
         link: { source: link.source, target: link.target, kind: link.kind },
         message: tx(ORCHESTRATOR_TEXTS.extensionErrorLinkKindNotDeclared, {
           extractorId: qualifiedId,
           linkKind: link.kind,
-          declaredKinds: extractor.emitsLinkKinds.join(", ")
+          declaredKinds: knownKinds.join(", ")
         })
       })
     );
     return null;
   }
-  const confidence = link.confidence ?? extractor.defaultConfidence;
+  const confidence = link.confidence ?? "medium";
   return { ...link, confidence };
 }
 function dedupeLinks(links) {
@@ -901,7 +903,7 @@ async function runAnalyzers(analyzers, nodes, internalLinks, orphanSidecars, sid
   const issues = [];
   const contributions = [];
   const validators = loadSchemaValidators();
-  validateRecommendedActions(analyzers, registeredActionIds, emitter);
+  void registeredActionIds;
   const analyzerOrphans = orphanSidecars.map((o) => ({
     relativePath: o.relativePath,
     expectedMdPath: o.expectedMdPath
@@ -973,27 +975,6 @@ async function runAnalyzers(analyzers, nodes, internalLinks, orphanSidecars, sid
   }
   return { issues, contributions };
 }
-function validateRecommendedActions(analyzers, registeredActionIds, emitter) {
-  for (const analyzer of analyzers) {
-    const refs = analyzer.recommendedActions;
-    if (refs === void 0 || refs.length === 0) continue;
-    const analyzerId = qualifiedExtensionId(analyzer.pluginId, analyzer.id);
-    for (const actionId of refs) {
-      if (registeredActionIds.has(actionId)) continue;
-      emitter.emit(
-        makeEvent("extension.error", {
-          kind: "recommended-action-missing",
-          extensionId: analyzerId,
-          actionId,
-          message: tx(ORCHESTRATOR_TEXTS.extensionErrorRecommendedActionMissing, {
-            analyzerId,
-            actionId
-          })
-        })
-      );
-    }
-  }
-}
 function validateIssue(analyzer, issue, emitter) {
   const severity = issue.severity;
   if (severity !== "error" && severity !== "warn" && severity !== "info") {
@@ -1071,9 +1052,15 @@ function originatingNodeOf(link, priorNodePaths) {
   return link.source;
 }
 function computeCacheDecision(opts) {
-  const applicableExtractors = opts.extractors.filter(
-    (ex) => ex.applicableKinds === void 0 || ex.applicableKinds.includes(opts.kind)
-  );
+  const applicableExtractors = opts.extractors.filter((ex) => {
+    const kinds = ex.precondition?.kind;
+    if (!kinds || kinds.length === 0) return true;
+    return kinds.some((qualified) => {
+      const slashIdx = qualified.indexOf("/");
+      const kindOnly = slashIdx === -1 ? qualified : qualified.slice(slashIdx + 1);
+      return kindOnly === opts.kind;
+    });
+  });
   const applicableQualifiedIds = new Set(
     applicableExtractors.map((ex) => qualifiedExtensionId(ex.pluginId, ex.id))
   );
@@ -1264,6 +1251,7 @@ function flagAmbiguousRenames(opts) {
 function flagOrphans(opts) {
   for (const fromPath of opts.deletedPaths) {
     if (opts.claimedDeleted.has(fromPath)) continue;
+    if (opts.silenced?.(fromPath)) continue;
     opts.issues.push({
       analyzerId: "orphan",
       severity: "info",
@@ -1273,7 +1261,7 @@ function flagOrphans(opts) {
     });
   }
 }
-function detectRenamesAndOrphans(prior, current, issues) {
+function detectRenamesAndOrphans(prior, current, issues, silenced) {
   const priorByPath = /* @__PURE__ */ new Map();
   for (const n of prior.nodes) priorByPath.set(n.path, n);
   const currentByPath = /* @__PURE__ */ new Map();
@@ -1307,17 +1295,22 @@ function detectRenamesAndOrphans(prior, current, issues) {
     issues
   }));
   flagAmbiguousRenames({ newPaths, candidatesByNew, claimedDeleted, claimedNew, issues });
-  flagOrphans({ deletedPaths, claimedDeleted, issues });
+  flagOrphans({
+    deletedPaths,
+    claimedDeleted,
+    issues,
+    ...silenced ? { silenced } : {}
+  });
   return ops;
 }
 
 // kernel/scan/walk-content.ts
 import { readFile, readdir, lstat } from "fs/promises";
-import { join as join2, relative as relative2, sep } from "path";
+import { join as join3, relative as relative2, sep } from "path";
 
 // kernel/scan/ignore.ts
-import { existsSync as existsSync2, readFileSync as readFileSync4 } from "fs";
-import { dirname as dirname2, resolve as resolve5 } from "path";
+import { existsSync as existsSync3, readFileSync as readFileSync5 } from "fs";
+import { dirname as dirname3, resolve as resolve5 } from "path";
 import { fileURLToPath } from "url";
 import ignoreFactory from "ignore";
 function buildIgnoreFilter(opts = {}) {
@@ -1349,7 +1342,7 @@ function loadDefaultsText() {
   return cachedDefaults;
 }
 function readDefaultsFromDisk() {
-  const here = dirname2(fileURLToPath(import.meta.url));
+  const here = dirname3(fileURLToPath(import.meta.url));
   const candidates = [
     resolve5(here, "../../config/defaults/skillmapignore"),
     // src/kernel/scan/ → src/config/defaults/
@@ -1358,9 +1351,9 @@ function readDefaultsFromDisk() {
     resolve5(here, "config/defaults/skillmapignore")
   ];
   for (const candidate of candidates) {
-    if (existsSync2(candidate)) {
+    if (existsSync3(candidate)) {
       try {
-        return readFileSync4(candidate, "utf8");
+        return readFileSync5(candidate, "utf8");
       } catch {
       }
     }
@@ -1368,7 +1361,7 @@ function readDefaultsFromDisk() {
   return "";
 }
 
-// built-in-plugins/parsers/frontmatter-yaml/index.ts
+// plugins/core/parsers/frontmatter-yaml/index.ts
 import yaml from "js-yaml";
 
 // kernel/util/strip-prototype-pollution.ts
@@ -1392,7 +1385,7 @@ function strip(value) {
   return out;
 }
 
-// built-in-plugins/parsers/frontmatter-yaml/index.ts
+// plugins/core/parsers/frontmatter-yaml/index.ts
 var FRONTMATTER_RE = /^---\r?\n([\s\S]*?)\r?\n---\r?\n?([\s\S]*)$/;
 var frontmatterYamlParser = {
   id: "frontmatter-yaml",
@@ -1426,7 +1419,7 @@ function sanitiseParseErrorMessage(err) {
   return raw.replace(/[-]+/g, " ").replace(/\s+/g, " ").trim();
 }
 
-// built-in-plugins/parsers/plain/index.ts
+// plugins/core/parsers/plain/index.ts
 var plainParser = {
   id: "plain",
   parse(raw, _path) {
@@ -1489,7 +1482,7 @@ async function* walkRoot(root, current, filter, extensions) {
   }
   for (const entry of entries) {
     const name = entry.name;
-    const full = join2(current, name);
+    const full = join3(current, name);
     const rel = relative2(root, full).split(sep).join("/");
     if (filter.ignores(rel)) continue;
     if (entry.isSymbolicLink()) continue;
@@ -1533,19 +1526,19 @@ function resolveProviderWalk(provider) {
 }
 
 // kernel/sidecar/parse.ts
-import { existsSync as existsSync3, readFileSync as readFileSync5 } from "fs";
-import { dirname as dirname3, resolve as resolve6 } from "path";
+import { existsSync as existsSync4, readFileSync as readFileSync6 } from "fs";
+import { dirname as dirname4, resolve as resolve6 } from "path";
 import { createRequire as createRequire3 } from "module";
 import { Ajv2020 as Ajv20204 } from "ajv/dist/2020.js";
 import yaml2 from "js-yaml";
 function readSidecarFor(mdAbsolutePath) {
   const sidecarPath = sidecarPathFor(mdAbsolutePath);
-  if (!existsSync3(sidecarPath)) {
+  if (!existsSync4(sidecarPath)) {
     return { parsed: null, present: false, issues: [] };
   }
   let raw;
   try {
-    raw = readFileSync5(sidecarPath, "utf8");
+    raw = readFileSync6(sidecarPath, "utf8");
   } catch (err) {
     return {
       parsed: null,
@@ -1613,10 +1606,10 @@ function getSidecarValidator() {
   applyAjvFormats(ajv);
   const specRoot = resolveSpecRoot2();
   const annotationsSchema = JSON.parse(
-    readFileSync5(resolve6(specRoot, "schemas/annotations.schema.json"), "utf8")
+    readFileSync6(resolve6(specRoot, "schemas/annotations.schema.json"), "utf8")
   );
   const sidecarSchema = JSON.parse(
-    readFileSync5(resolve6(specRoot, "schemas/sidecar.schema.json"), "utf8")
+    readFileSync6(resolve6(specRoot, "schemas/sidecar.schema.json"), "utf8")
   );
   ajv.addSchema(annotationsSchema);
   cachedSidecarValidator = ajv.compile(sidecarSchema);
@@ -1626,7 +1619,7 @@ function resolveSpecRoot2() {
   const require2 = createRequire3(import.meta.url);
   try {
     const indexPath = require2.resolve("@skill-map/spec/index.json");
-    return dirname3(indexPath);
+    return dirname4(indexPath);
   } catch {
     throw new Error(
       "@skill-map/spec not resolvable: sidecar reader cannot load schemas."
@@ -1645,8 +1638,8 @@ function computeDriftStatus(args) {
 }
 
 // kernel/sidecar/discover-orphans.ts
-import { existsSync as existsSync4, readdirSync as readdirSync2, statSync } from "fs";
-import { join as join3, relative as relative3, sep as sep2 } from "path";
+import { existsSync as existsSync5, readdirSync as readdirSync3, statSync as statSync3 } from "fs";
+import { join as join4, relative as relative3, sep as sep2 } from "path";
 function discoverOrphanSidecars(roots, shouldSkip) {
   const out = [];
   for (const root of roots) {
@@ -1657,12 +1650,12 @@ function discoverOrphanSidecars(roots, shouldSkip) {
 function walk(root, current, shouldSkip, out) {
   let entries;
   try {
-    entries = readdirSync2(current, { withFileTypes: true, encoding: "utf8" });
+    entries = readdirSync3(current, { withFileTypes: true, encoding: "utf8" });
   } catch {
     return;
   }
   for (const entry of entries) {
-    const full = join3(current, entry.name);
+    const full = join4(current, entry.name);
     const rel = relative3(root, full).split(sep2).join("/");
     if (shouldSkip(rel)) continue;
     if (entry.isSymbolicLink()) continue;
@@ -1673,21 +1666,21 @@ function walk(root, current, shouldSkip, out) {
     if (!entry.isFile()) continue;
     if (!entry.name.endsWith(".sm")) continue;
     const expectedMd = `${full.slice(0, -".sm".length)}.md`;
-    if (existsSync4(expectedMd) && safeIsFile(expectedMd)) continue;
+    if (existsSync5(expectedMd) && safeIsFile(expectedMd)) continue;
     out.push({ sidecarPath: full, relativePath: rel, expectedMdPath: expectedMd });
   }
 }
 function safeIsFile(path) {
   try {
-    return statSync(path).isFile();
+    return statSync3(path).isFile();
   } catch {
     return false;
   }
 }
 
 // kernel/sidecar/store.ts
-import { existsSync as existsSync7, readFileSync as readFileSync8 } from "fs";
-import { dirname as dirname5, resolve as resolve9 } from "path";
+import { existsSync as existsSync8, readFileSync as readFileSync9 } from "fs";
+import { dirname as dirname6, resolve as resolve9 } from "path";
 import { createRequire as createRequire4 } from "module";
 import { Ajv2020 as Ajv20205 } from "ajv/dist/2020.js";
 import yaml3 from "js-yaml";
@@ -1696,29 +1689,29 @@ import yaml3 from "js-yaml";
 import {
   closeSync,
   constants as fsConstants,
-  existsSync as existsSync5,
+  existsSync as existsSync6,
   mkdirSync,
   openSync,
-  readFileSync as readFileSync6,
+  readFileSync as readFileSync7,
   renameSync,
   unlinkSync,
   writeSync
 } from "fs";
 import { randomBytes } from "crypto";
-import { dirname as dirname4 } from "path";
+import { dirname as dirname5 } from "path";
 
 // core/config/helper.ts
 import { homedir as osHomedir } from "os";
-import { isAbsolute as isAbsolute2, join as join6, resolve as resolve8 } from "path";
+import { isAbsolute as isAbsolute2, join as join7, resolve as resolve8 } from "path";
 
 // kernel/config/loader.ts
-import { existsSync as existsSync6, readFileSync as readFileSync7 } from "fs";
+import { existsSync as existsSync7, readFileSync as readFileSync8 } from "fs";
 
 // kernel/util/skill-map-paths.ts
-import { join as join5 } from "path";
+import { join as join6 } from "path";
 
 // core/paths/db-path.ts
-import { join as join4, resolve as resolve7 } from "path";
+import { join as join5, resolve as resolve7 } from "path";
 var SKILL_MAP_DIR = ".skill-map";
 var DB_FILENAME = "skill-map.db";
 var LOCAL_SETTINGS_FILENAME = "settings.local.json";
@@ -1730,7 +1723,7 @@ var GITIGNORE_ENTRIES = [
 
 // kernel/orchestrator/node-build.ts
 import { createHash } from "crypto";
-import { existsSync as existsSync8 } from "fs";
+import { existsSync as existsSync9 } from "fs";
 import { isAbsolute as isAbsolute3, resolve as resolvePath } from "path";
 import "js-tiktoken/lite";
 import yaml4 from "js-yaml";
@@ -1894,11 +1887,11 @@ function resolveSidecarOverlay(relativePath, nodePathForIssue, roots, liveBodyHa
 }
 function resolveAbsoluteMdPath(relativePath, roots) {
   if (isAbsolute3(relativePath)) {
-    return existsSync8(relativePath) ? relativePath : null;
+    return existsSync9(relativePath) ? relativePath : null;
   }
   for (const root of roots) {
     const candidate = resolvePath(root, relativePath);
-    if (existsSync8(candidate)) return candidate;
+    if (existsSync9(candidate)) return candidate;
   }
   return null;
 }
@@ -2027,6 +2020,9 @@ function buildWalkContext(opts) {
 async function processRawNode(raw, provider, wctx, accum, claimedPaths, nextIndex) {
   const bodyHash = sha256(raw.body);
   const frontmatterHash = sha256(canonicalFrontmatter(raw.frontmatter, raw.frontmatterRaw));
+  if (Array.isArray(provider.roots) && provider.roots.length > 0) {
+    if (!matchesAnyRoot(raw.path, provider.roots)) return false;
+  }
   const kind = provider.classify(raw.path, raw.frontmatter);
   if (kind === null) {
     return false;
@@ -2195,6 +2191,26 @@ function recordExtractorRuns(nodePath, ctx, accum) {
     });
   }
 }
+function matchesAnyRoot(relPath, roots) {
+  for (const r of roots) {
+    if (matchesOneRoot(relPath, r)) return true;
+  }
+  return false;
+}
+function matchesOneRoot(relPath, pattern) {
+  if (pattern.endsWith("/**")) return matchesDeepGlob(relPath, pattern.slice(0, -3));
+  if (pattern.endsWith("/*")) return matchesShallowGlob(relPath, pattern.slice(0, -2));
+  return relPath === pattern;
+}
+function matchesDeepGlob(relPath, prefix) {
+  if (prefix.length === 0) return true;
+  return relPath === prefix || relPath.startsWith(`${prefix}/`);
+}
+function matchesShallowGlob(relPath, prefix) {
+  if (!relPath.startsWith(`${prefix}/`)) return false;
+  const tail = relPath.slice(prefix.length + 1);
+  return tail.length > 0 && !tail.includes("/");
+}
 
 // kernel/orchestrator/index.ts
 var SCANNED_BY = {
@@ -2263,7 +2279,8 @@ async function runScanInternal(_kernel, options) {
   mergeAnalyzerEmissions(walked, analyzerResult, exts.analyzers);
   const issues = analyzerResult.issues;
   for (const issue of walked.frontmatterIssues) issues.push(issue);
-  const renameOps = prior ? detectRenamesAndOrphans(prior, walked.nodes, issues) : [];
+  const silenced = options.ignoreFilter ? (path) => options.ignoreFilter.ignores(path) : void 0;
+  const renameOps = prior ? detectRenamesAndOrphans(prior, walked.nodes, issues, silenced) : [];
   const stats = buildScanStats(walked, issues, start);
   const scanCompletedEvent = makeEvent("scan.completed", { stats });
   emitter.emit(scanCompletedEvent);
@@ -2306,7 +2323,7 @@ async function dispatchExtractorCompleted(extractors, emitter, hookDispatcher) {
 function mergeAnalyzerEmissions(walked, analyzerResult, analyzers) {
   for (const c of analyzerResult.contributions) walked.contributions.push(c);
   for (const analyzer of analyzers ?? []) {
-    if (analyzer.viewContributions === void 0) continue;
+    if (analyzer.ui === void 0) continue;
     for (const node of walked.nodes) {
       walked.freshlyRunTuples.add(`${analyzer.pluginId}\0${analyzer.id}\0${node.path}`);
     }
@@ -2353,7 +2370,7 @@ function validateRoots(roots) {
     throw new Error(ORCHESTRATOR_TEXTS.runScanRootEmptyArray);
   }
   for (const root of roots) {
-    if (!existsSync9(root) || !statSync2(root).isDirectory()) {
+    if (!existsSync10(root) || !statSync4(root).isDirectory()) {
       throw new Error(tx(ORCHESTRATOR_TEXTS.runScanRootMissing, { root }));
     }
   }