@vibe-agent-toolkit/cli 0.2.0-rc.6 → 0.2.0-rc.7

package/dist/commands/verify.d.ts

@@ -15,10 +15,11 @@
  * Both sets are config-gated, and both are announced on startup.
  */
 import type { ProjectConfig } from '@vibe-agent-toolkit/resources';
-import { type ValidationIssue } from '@vibe-agent-toolkit/schema';
+import { type SeverityCounts, type ValidationIssue } from '@vibe-agent-toolkit/schema';
 import { Command } from 'commander';
+import type { createLogger } from '../utils/logger.js';
 import { type ConsistencyIssueSeverity } from './consistency-check.js';
-import { type PhaseSelection } from './phase-utils.js';
+import { type PhaseResult, type PhaseSelection } from './phase-utils.js';
 import type { DiscoveredSkill } from './skills/command-helpers.js';
 export interface VerifyCommandOptions {
     /** Retired; declared only so {@link rejectRetiredOnly} can explain the removal. */
@@ -82,10 +83,32 @@ export declare function checkFilesConfigDests(cwd: string, discovered: readonly
  *
  * Locations anchor at `cwd`, the run's stated root, so a reader can open them.
  *
+ * Returns the count of bundles crawled beside the findings, because the phase
+ * that publishes them needs the denominator: zero findings over zero bundles is
+ * not a pass — see {@link buildPackagedContentPhase}.
+ *
  * @param discovered - The skills this run discovered from `skills.include`. See
  *   {@link collectBuiltSkillOutputs} for why it is required rather than optional.
  */
-export declare function checkPackagedAgentInstructionFiles(cwd: string, discovered: readonly DiscoveredSkill[]): ValidationIssue[];
+export declare function checkPackagedAgentInstructionFiles(cwd: string, discovered: readonly DiscoveredSkill[]): PackagedContentCrawl;
+/**
+ * What the packaged-content crawl found, over how many bundles, and how many
+ * it should have found.
+ *
+ * `bundlesInspected` can exceed `bundlesExpected`: a bundle sitting in `dist/`
+ * for a `skills.config` key discovery no longer reaches is inspected (it is
+ * distributed output) but not expected (nothing in this run builds it). It can
+ * fall short of it only by the bundles named in `bundlesMissing`.
+ */
+export interface PackagedContentCrawl {
+    /** Built bundles that EXIST on disk and were crawled — the phase's denominator. */
+    bundlesInspected: number;
+    /** Bundles `vat build` produces for this run's discovered skills — what the denominator should be. */
+    bundlesExpected: number;
+    /** Expected bundles absent from disk, as `cwd`-relative paths. Non-empty means the phase is not a verdict. */
+    bundlesMissing: string[];
+    issues: ValidationIssue[];
+}
 /**
  * Decide which verification phases to run.
  *
@@ -140,5 +163,73 @@ interface PublishedIssue {
  * and stderr is not the document a CI consumer parses.
  */
 export declare function toPublishedIssue(issue: ValidationIssue): PublishedIssue;
+/**
+ * A phase result that carries its own findings into the archived YAML.
+ *
+ * Extends {@link PhaseResult} rather than widening it: only verify's own phases
+ * hold findings — a delegated phase's findings belong to (and are printed by)
+ * the command it delegates to, inside the report nested under `report`.
+ */
+interface FindingsPhaseResult extends PhaseResult {
+    issueCounts: SeverityCounts;
+    issues: PublishedIssue[];
+}
+/**
+ * The `packaged-content` phase's result: its findings, the count they are
+ * over, and the count they should have been over — see {@link PackagedContentCrawl}.
+ */
+export interface PackagedContentPhaseResult extends FindingsPhaseResult {
+    bundlesInspected: number;
+    bundlesExpected: number;
+    bundlesMissing: string[];
+}
+/**
+ * Build the `packaged-content` phase result from what the crawl found.
+ *
+ * 🚨 **Zero bundles is an ERROR, not a clean phase — and so is a MISSING one.**
+ * The phase is pushed unconditionally whenever `skills:` exists and it feeds the
+ * real exit code; `discoverSkillsFromConfig` returning `[]` on a typo'd glob —
+ * or `dist/` not having been built at all, or built somewhere else — gave the
+ * crawl nothing to walk, and nothing walked was zero findings was `success`,
+ * with no count in the document to say the phase had looked at nothing. `vat
+ * verify` exists to check the BUILT tree; a run that found none of it is not a
+ * verdict on it. Nor is a run that found half of it: with `bundlesInspected` as
+ * the only denominator, two discovered skills and one deleted bundle published
+ * `success` beside `bundlesInspected: 1`. The crawl now also carries what it
+ * should have found, and the document publishes both counts.
+ *
+ * Derived here, in the one function that produces this phase's document, and
+ * not in the command body, so no path through the orchestrator can publish
+ * `status: success` beside `bundlesInspected: 0` or beside a non-empty
+ * `bundlesMissing`. Through the shared mechanism in `run-integrity.ts`: one
+ * non-overridable `RESOURCE_CHECK_BROKEN` at `error`, which
+ * {@link exitCodeForPhases} then turns into exit 1. ONE, not two, when both
+ * apply: the missing-bundle refusal is derived first because it names paths,
+ * and {@link nothingCheckedFinding} stands down behind an existing
+ * run-integrity finding.
+ *
+ * Pure, and exported so the refusal is pinned without a project on disk.
+ */
+export declare function buildPackagedContentPhase(crawl: PackagedContentCrawl): PackagedContentPhaseResult;
+/**
+ * Run the `packaged-content` phase: crawl, derive the phase document, and
+ * report THAT document's issues on stderr.
+ *
+ * 🚨 **The stderr report used to be gated on the crawl, one line before the
+ * refusal was derived.** `if (crawl.issues.length > 0) report(crawl.issues)`
+ * ran ahead of {@link buildPackagedContentPhase}, which is where the
+ * zero-bundle refusal is added — so on an unbuilt project the crawl found
+ * nothing, nothing was logged, the skills phase's `✅ All validations passed`
+ * stayed the last line on stderr, and the process exited 1 on a refusal that
+ * existed only in the YAML. Reporting from the phase result makes what stderr
+ * says and what the exit code is computed from one list, which is
+ * `run-integrity.ts` invariant 6.
+ *
+ * The round trip through `asValidationIssues` is deliberate rather than
+ * reporting the crawl's list plus a second derivation of the refusal: the
+ * document is the artifact of record, and stderr should render exactly what it
+ * carries, not a parallel computation that can drift from it.
+ */
+export declare function runPackagedContentPhase(projectRoot: string, discoveredSkills: readonly DiscoveredSkill[], logger: ReturnType<typeof createLogger>): PackagedContentPhaseResult;
 export {};
 //# sourceMappingURL=verify.d.ts.map

package/dist/commands/verify.d.ts.map

@@ -1 +1 @@
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+{"version":3,"file":"verify.d.ts","sourceRoot":"","sources":["../../src/commands/verify.ts"],"names":[],"mappings":"AAAA;;;;;;;;;;;;;;;GAeG;AAWH,OAAO,KAAK,EAAE,aAAa,EAAE,MAAM,+BAA+B,CAAC;AACnE,OAAO,EAGL,KAAK,cAAc,EACnB,KAAK,eAAe,EACrB,MAAM,4BAA4B,CAAC;AAEpC,OAAO,EAAE,OAAO,EAAE,MAAM,WAAW,CAAC;AAMpC,OAAO,KAAK,EAAE,YAAY,EAAE,MAAM,oBAAoB,CAAC;AAOvD,OAAO,EAGL,KAAK,wBAAwB,EAC9B,MAAM,wBAAwB,CAAC;AAChC,OAAO,EAUL,KAAK,WAAW,EAChB,KAAK,cAAc,EAEpB,MAAM,kBAAkB,CAAC;AAG1B,OAAO,KAAK,EAAE,eAAe,EAAE,MAAM,6BAA6B,CAAC;AAInE,MAAM,WAAW,oBAAoB;IACnC,mFAAmF;IACnF,IAAI,CAAC,EAAE,MAAM,CAAC;IACd,OAAO,CAAC,EAAE,OAAO,CAAC;IAClB,KAAK,CAAC,EAAE,OAAO,CAAC;CACjB;AAYD,wBAAgB,2BAA2B,IAAI,OAAO,CA4FrD;AAED,iFAAiF;AACjF,MAAM,WAAW,oBAAoB;IACnC,SAAS,EAAE,MAAM,CAAC;IAClB,kFAAkF;IAClF,SAAS,EAAE,MAAM,CAAC;IAClB,OAAO,EAAE,MAAM,EAAE,CAAC;CACnB;AAsMD;;;;;;;;;GASG;AACH,wBAAgB,qBAAqB,CACnC,GAAG,EAAE,MAAM,EACX,UAAU,EAAE,SAAS,eAAe,EAAE,GACrC,oBAAoB,EAAE,CAmBxB;AAED;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;GA2CG;AACH,wBAAgB,kCAAkC,CAChD,GAAG,EAAE,MAAM,EACX,UAAU,EAAE,SAAS,eAAe,EAAE,GACrC,oBAAoB,CAiBtB;AAED;;;;;;;;GAQG;AACH,MAAM,WAAW,oBAAoB;IACnC,mFAAmF;IACnF,gBAAgB,EAAE,MAAM,CAAC;IACzB,sGAAsG;IACtG,eAAe,EAAE,MAAM,CAAC;IACxB,8GAA8G;IAC9G,cAAc,EAAE,MAAM,EAAE,CAAC;IACzB,MAAM,EAAE,eAAe,EAAE,CAAC;CAC3B;AAwGD;;;;;;;;;;;;;;;;;;;;;GAqBG;AACH,wBAAgB,kBAAkB,CAChC,MAAM,EAAE,aAAa,GAAG,SAAS,EACjC,WAAW,CAAC,EAAE,MAAM,EACpB,OAAO,CAAC,EAAE,OAAO,GAChB,cAAc,CAiChB;AA4CD;;;GAGG;AACH,wBAAgB,wBAAwB,CACtC,mBAAmB,EAAE,SAAS,MAAM,EAAE,EACtC,MAAM,EAAE,aAAa,GAAG,SAAS,GAChC,MAAM,CAGR;AAED,wEAAwE;AACxE,UAAU,cAAc;IAGtB,QAAQ,EAAE,eAAe,CAAC,UAAU,CAAC,GAAG,wBAAwB,CAAC;IACjE,IAAI,EAAE,MAAM,CAAC;IACb,OAAO,EAAE,MAAM,CAAC;IAChB,GAAG,EAAE,MAAM,CAAC;IACZ,mFAAmF;IACnF,QAAQ,CAAC,EAAE,MAAM,CAAC;IAClB,2DAA2D;IAC3D,IAAI,CAAC,EAAE,MAAM,CAAC;IACd,kDAAkD;IAClD,SAAS,CAAC,EAAE,MAAM,CAAC;CACpB;AAED;;;;;;;;;;;GAWG;AACH,wBAAgB,gBAAgB,CAAC,KAAK,EAAE,eAAe,GAAG,cAAc,CAavE;AAED;;;;;;GAMG;AACH,UAAU,mBAAoB,SAAQ,WAAW;IAC/C,WAAW,EAAE,cAAc,CAAC;IAC5B,MAAM,EAAE,cAAc,EAAE,CAAC;CAC1B;AAED;;;GAGG;AACH,MAAM,WAAW,0BAA2B,SAAQ,mBAAmB;IACrE,gBAAgB,EAAE,MAAM,CAAC;IACzB,eAAe,EAAE,MAAM,CAAC;IACxB,cAAc,EAAE,MAAM,EAAE,CAAC;CAC1B;AA0BD;;;;;;;;;;;;;;;;;;;;;;;;;;GA0BG;AACH,wBAAgB,yBAAyB,CAAC,KAAK,EAAE,oBAAoB,GAAG,0BAA0B,CAwBjG;AAmBD;;;;;;;;;;;;;;;;;;GAkBG;AACH,wBAAgB,uBAAuB,CACrC,WAAW,EAAE,MAAM,EACnB,gBAAgB,EAAE,SAAS,eAAe,EAAE,EAC5C,MAAM,EAAE,UAAU,CAAC,OAAO,YAAY,CAAC,GACtC,0BAA0B,CAO5B"}

package/dist/commands/verify.js

@@ -14,11 +14,11 @@
  * are chosen by `selectInProcessVerifyPhases`. Every phase runs in this process.
  * Both sets are config-gated, and both are announced on startup.
  */
-import { existsSync } from 'node:fs';
+import { existsSync, statSync } from 'node:fs';
 import { basename } from 'node:path';
 import { computeTreeCopiedSkillLocations, detectPackagedAgentInstructionFiles, explicitFilesConfigDests, } from '@vibe-agent-toolkit/agent-skills';
 import { calculateValidationStatus, countBySeverity, } from '@vibe-agent-toolkit/schema';
-import { safePath } from '@vibe-agent-toolkit/utils';
+import { safePath, toForwardSlash } from '@vibe-agent-toolkit/utils';
 import { Command } from 'commander';
 import { handleCommandError } from '../utils/command-error.js';
 import { loadConfig } from '../utils/config-loader.js';
@@ -26,6 +26,7 @@ import { formatIssueLines } from '../utils/issue-rendering.js';
 import { resolveIssueSeverity } from '../utils/issue-severity.js';
 import { writeYamlOutput } from '../utils/output.js';
 import { requireProjectRoot } from '../utils/project-root-policy.js';
+import { nothingCheckedFinding, runIntegrityFinding } from '../utils/run-integrity.js';
 import { mergeSkillPackagingConfig } from '../utils/skill-packaging-config.js';
 import { runMarketplaceValidatePhase } from './claude/marketplace/validate.js';
 import { runConsistencyChecks, } from './consistency-check.js';
@@ -93,7 +94,14 @@ Output:
     publish issueCounts {errors, warnings, info}; 'consistency' and
     'packaged-content' carry their findings into the document too, while
     'files-config-dests' publishes counts only and lists the missing dests on
-    stderr.
+    stderr. 'packaged-content' also publishes bundlesInspected — the built
+    bundles it crawled — beside bundlesExpected (the bundles 'vat build'
+    produces for the skills this run discovered) and bundlesMissing (expected
+    bundles absent from dist/, by path). Zero inspected, or any missing, is
+    refused as RESOURCE_CHECK_BROKEN at error (exit 1) rather than reported as
+    a pass: a run that found none of the build (dist/ not built, or a
+    skills.include glob that matched nothing) or only part of it (a bundle
+    deleted, a skill added since the last build) is not a verdict on what ships.
   Progress and validation errors → stderr (streamed live)
 
   By default each delegated phase reports a per-asset summary plus the assets
@@ -135,11 +143,29 @@ function filesOf(entry) {
     return entry.packaging.files ?? [];
 }
 /**
- * Register a check for (skillName, outputDir, packaging) in the dedup map.
+ * Whether `dir` is a directory — `false` for a file, for nothing, and for a
+ * path the process cannot stat. All three are "no bundle here": a bundle is a
+ * tree, and a regular FILE sitting where one should be passed `existsSync`,
+ * was counted as built, and the packaged-content crawl then threw `Base path is
+ * not a directory: /abs/…` out of the whole command — exit 2, no document, an
+ * absolute path on stderr — where the missing-bundle lane names it at exit 1.
+ */
+function isDirectory(dir) {
+    try {
+        // eslint-disable-next-line security/detect-non-literal-fs-filename -- outputDir is resolved from config, not user input
+        return statSync(dir).isDirectory();
+    }
+    catch {
+        return false;
+    }
+}
+/**
+ * Register a (skillName, outputDir, packaging) candidate.
  *
- * Skips silently if:
- *   - outputDir does not exist on disk (not a candidate)
- *   - the key was already added (dedup guard)
+ * A candidate whose output dir IS A DIRECTORY lands in `built` (deduplicated by
+ * key). An `expected` candidate is counted whether or not it exists, and one
+ * that is not a directory is named in `missing` — that absence is the finding,
+ * not a skip (see {@link isDirectory} for why "exists" is not enough).
  *
  * An EMPTY `files:` block is registered, not skipped: {@link checkFilesConfigDests}
  * has nothing to verify for such a skill and filters it out itself, but
@@ -147,27 +173,33 @@ function filesOf(entry) {
  * with no `files:` block is exactly the one whose agent-instruction file arrived by
  * some other route, and dropping it here would make the crawl blind to it.
  */
-function tryAddCheckEntry(checks, skillName, outputDir, packaging) {
-    // eslint-disable-next-line security/detect-non-literal-fs-filename -- outputDir is resolved from config, not user input
-    if (!existsSync(outputDir))
+function addCheckCandidate(outputs, seen, cwd, candidate, expected) {
+    const key = `${candidate.skillName}\0${candidate.outputDir}`;
+    if (seen.has(key))
         return;
-    const key = `${skillName}\0${outputDir}`;
-    if (!checks.has(key)) {
-        checks.set(key, { skillName, outputDir, packaging });
-    }
+    seen.add(key);
+    const exists = isDirectory(candidate.outputDir);
+    if (exists)
+        outputs.built.push(candidate);
+    if (!expected)
+        return;
+    outputs.expected += 1;
+    if (!exists)
+        outputs.missing.push(toForwardSlash(safePath.relative(cwd, candidate.outputDir)));
 }
 /**
- * Every built skill bundle this project's config accounts for that EXISTS on disk,
- * with the `files:` entries that govern it.
+ * Every built skill bundle this project's config accounts for, with the `files:`
+ * entries that govern it — those that EXIST on disk, and the coverage of those
+ * the build should have produced (see {@link BuiltSkillOutputs}).
  *
  * ONE enumeration of "where did `vat build` write this skill", shared by every
  * in-process verify phase, in the two locations the build actually uses:
  *   - Pool skills: `dist/skills/<fsName>/`
  *   - Tree-copy skills: `dist/.claude/plugins/.../skills/<name>/`
  *
- * Returns `[]` (never throws) for an unreadable config: `vat verify`'s delegated
- * phases report the real config error, and one of verify's own phases must not
- * race them with a second, worse diagnosis.
+ * Returns an empty enumeration (never throws) for an unreadable config: `vat
+ * verify`'s delegated phases report the real config error, and one of verify's
+ * own phases must not race them with a second, worse diagnosis.
  *
  * The pool arm enumerates the skills the run DISCOVERED, unioned with the keys of
  * `skills.config`. It used to be the config keys alone, which made both in-process
@@ -197,37 +229,44 @@ function tryAddCheckEntry(checks, skillName, outputDir, packaging) {
  * this command.
  */
 function collectBuiltSkillOutputs(cwd, discovered) {
+    const outputs = { built: [], expected: 0, missing: [] };
     try {
         const config = loadConfig(cwd);
         if (!config)
-            return [];
+            return outputs;
         const skillsConfig = config.skills;
         const defaults = skillsConfig?.defaults;
-        // Dedup map: key = `skillName\0outputDir` → check entry
-        const checks = new Map();
+        // Dedup guard: key = `skillName\0outputDir`
+        const seen = new Set();
         // --- Pool skills: candidate dir is dist/skills/<fsName> ---
-        const poolNames = new Set([
-            ...discovered.map((skill) => skill.name),
-            ...Object.keys(skillsConfig?.config ?? {}),
-        ]);
+        // Expected only when discovered: `vat skills build` builds every discovered
+        // skill and nothing else (see BuiltSkillOutputs.expected).
+        const discoveredNames = new Set(discovered.map((skill) => skill.name));
+        const poolNames = new Set([...discoveredNames, ...Object.keys(skillsConfig?.config ?? {})]);
         for (const skillName of poolNames) {
             const perSkill = skillsConfig?.config?.[skillName];
             const outputDir = safePath.resolve(cwd, 'dist', 'skills', skillNameToFsPath(skillName));
-            tryAddCheckEntry(checks, skillName, outputDir, mergeSkillPackagingConfig(defaults, perSkill));
+            addCheckCandidate(outputs, seen, cwd, { skillName, outputDir, packaging: mergeSkillPackagingConfig(defaults, perSkill) }, discoveredNames.has(skillName));
         }
         // --- Tree-copy skills: candidate dirs are plugin output skill dirs ---
+        // Always expected: every location here is a plugin-local skill the claude
+        // build phase packages into the plugin tree.
         for (const loc of computeTreeCopiedSkillLocations(config, cwd)) {
             // Per-skill config is keyed by the skill's declared NAME. `skillDirPath` is a
             // path (`group/nested-skill` for a nested skill), so try its trailing segment
             // too — the spelling that matches for every skill whose dir is named after it.
             const dirLeaf = basename(loc.skillDirPath);
             const perSkill = (skillsConfig?.config?.[loc.skillDirPath] ?? skillsConfig?.config?.[dirLeaf]);
-            tryAddCheckEntry(checks, loc.skillDirPath, loc.skillOutputDir, mergeSkillPackagingConfig(defaults, perSkill));
+            addCheckCandidate(outputs, seen, cwd, {
+                skillName: loc.skillDirPath,
+                outputDir: loc.skillOutputDir,
+                packaging: mergeSkillPackagingConfig(defaults, perSkill),
+            }, true);
         }
-        return [...checks.values()];
+        return outputs;
     }
     catch {
-        return [];
+        return { built: [], expected: 0, missing: [] };
     }
 }
 /**
@@ -242,7 +281,7 @@ function collectBuiltSkillOutputs(cwd, discovered) {
  */
 export function checkFilesConfigDests(cwd, discovered) {
     const results = [];
-    for (const check of collectBuiltSkillOutputs(cwd, discovered)) {
+    for (const check of collectBuiltSkillOutputs(cwd, discovered).built) {
         const { skillName, outputDir } = check;
         const mergedFiles = filesOf(check);
         if (mergedFiles.length === 0)
@@ -298,16 +337,26 @@ export function checkFilesConfigDests(cwd, discovered) {
  *
  * Locations anchor at `cwd`, the run's stated root, so a reader can open them.
  *
+ * Returns the count of bundles crawled beside the findings, because the phase
+ * that publishes them needs the denominator: zero findings over zero bundles is
+ * not a pass — see {@link buildPackagedContentPhase}.
+ *
  * @param discovered - The skills this run discovered from `skills.include`. See
  *   {@link collectBuiltSkillOutputs} for why it is required rather than optional.
  */
 export function checkPackagedAgentInstructionFiles(cwd, discovered) {
     const issues = [];
-    for (const check of collectBuiltSkillOutputs(cwd, discovered)) {
+    const outputs = collectBuiltSkillOutputs(cwd, discovered);
+    for (const check of outputs.built) {
         const raw = detectPackagedAgentInstructionFiles(check.outputDir, cwd, explicitFilesConfigDests(filesOf(check)));
         issues.push(...resolveIssueSeverity(raw, check.packaging.validation));
     }
-    return issues;
+    return {
+        bundlesInspected: outputs.built.length,
+        bundlesExpected: outputs.expected,
+        bundlesMissing: outputs.missing,
+        issues,
+    };
 }
 /**
  * Load the project config without letting a broken one abort the command.
@@ -517,6 +566,79 @@ export function toPublishedIssue(issue) {
         ...(issue.reference === undefined ? {} : { reference: issue.reference }),
     };
 }
+/**
+ * The refusal for a crawl that found only PART of the build.
+ *
+ * Mirrors `unresolvedLocalPluginsFinding` in `claude/marketplace/validate.ts`:
+ * the count declared, the count checked, and the missing ones BY NAME — the
+ * operator's next move is to look at those paths, so the message carries them.
+ * ONE finding however many are missing (run-integrity invariant 4).
+ *
+ * @param crawl - What the crawl found, over what
+ * @returns The one finding, or nothing when every expected bundle was inspected
+ */
+function missingBundlesFinding(crawl) {
+    if (crawl.bundlesMissing.length === 0)
+        return [];
+    const named = crawl.bundlesMissing.map((dir) => `\`${dir}\``).join(', ');
+    return [runIntegrityFinding(`This run discovered skills that \`vat build\` produces ${crawl.bundlesExpected} bundle(s) for and`
+            + ` the packaged-content phase inspected ${crawl.bundlesInspected}, so this phase is not a verdict`
+            + ' on the build: a bundle that was never crawled reads the same as a clean one. Expected'
+            + ` bundle(s) not found on disk: ${named}. Usually \`vat build\` has not run since a skill was`
+            + ' added, failed part-way, or wrote somewhere other than dist/ — or the bundle was deleted.'
+            + ' Run `vat build` first, then re-run `vat verify`.')];
+}
+/**
+ * Build the `packaged-content` phase result from what the crawl found.
+ *
+ * 🚨 **Zero bundles is an ERROR, not a clean phase — and so is a MISSING one.**
+ * The phase is pushed unconditionally whenever `skills:` exists and it feeds the
+ * real exit code; `discoverSkillsFromConfig` returning `[]` on a typo'd glob —
+ * or `dist/` not having been built at all, or built somewhere else — gave the
+ * crawl nothing to walk, and nothing walked was zero findings was `success`,
+ * with no count in the document to say the phase had looked at nothing. `vat
+ * verify` exists to check the BUILT tree; a run that found none of it is not a
+ * verdict on it. Nor is a run that found half of it: with `bundlesInspected` as
+ * the only denominator, two discovered skills and one deleted bundle published
+ * `success` beside `bundlesInspected: 1`. The crawl now also carries what it
+ * should have found, and the document publishes both counts.
+ *
+ * Derived here, in the one function that produces this phase's document, and
+ * not in the command body, so no path through the orchestrator can publish
+ * `status: success` beside `bundlesInspected: 0` or beside a non-empty
+ * `bundlesMissing`. Through the shared mechanism in `run-integrity.ts`: one
+ * non-overridable `RESOURCE_CHECK_BROKEN` at `error`, which
+ * {@link exitCodeForPhases} then turns into exit 1. ONE, not two, when both
+ * apply: the missing-bundle refusal is derived first because it names paths,
+ * and {@link nothingCheckedFinding} stands down behind an existing
+ * run-integrity finding.
+ *
+ * Pure, and exported so the refusal is pinned without a project on disk.
+ */
+export function buildPackagedContentPhase(crawl) {
+    const { bundlesInspected, bundlesExpected, bundlesMissing, issues: found } = crawl;
+    const missing = missingBundlesFinding(crawl);
+    const issues = [
+        ...missing,
+        ...nothingCheckedFinding(bundlesInspected, [...missing, ...found], () => 'The packaged-content phase inspected 0 built skill bundles, so this phase is not a'
+            + ' verdict: nothing was crawled for files that must not ship, and the document reads'
+            + ' the same as a run over clean bundles. Either `vat build` has not run (or wrote'
+            + ' somewhere other than dist/), or `skills.include` in vibe-agent-toolkit.config.yaml'
+            + ' matched no SKILL.md — usually a typo in the glob. Run `vat build` first; `vat skills'
+            + ' validate` lists what the globs discover.'),
+        ...found,
+    ];
+    return {
+        name: PACKAGED_CONTENT,
+        status: calculateValidationStatus(issues),
+        // The denominator, beside the counts it qualifies — and what it should have been.
+        bundlesInspected,
+        bundlesExpected,
+        bundlesMissing,
+        issueCounts: countBySeverity(issues),
+        issues: issues.map(toPublishedIssue),
+    };
+}
 /**
  * `ConsistencyIssue` speaks the same severity vocabulary as `ValidationIssue`
  * but carries a free-form `code`, so it is counted through this projection —
@@ -529,8 +651,37 @@ function asValidationIssues(issues) {
         severity: issue.severity,
         message: issue.message,
         fix: issue.fix,
+        ...(issue.location === undefined ? {} : { location: issue.location }),
+        ...(issue.line === undefined ? {} : { line: issue.line }),
     }));
 }
+/**
+ * Run the `packaged-content` phase: crawl, derive the phase document, and
+ * report THAT document's issues on stderr.
+ *
+ * 🚨 **The stderr report used to be gated on the crawl, one line before the
+ * refusal was derived.** `if (crawl.issues.length > 0) report(crawl.issues)`
+ * ran ahead of {@link buildPackagedContentPhase}, which is where the
+ * zero-bundle refusal is added — so on an unbuilt project the crawl found
+ * nothing, nothing was logged, the skills phase's `✅ All validations passed`
+ * stayed the last line on stderr, and the process exited 1 on a refusal that
+ * existed only in the YAML. Reporting from the phase result makes what stderr
+ * says and what the exit code is computed from one list, which is
+ * `run-integrity.ts` invariant 6.
+ *
+ * The round trip through `asValidationIssues` is deliberate rather than
+ * reporting the crawl's list plus a second derivation of the refusal: the
+ * document is the artifact of record, and stderr should render exactly what it
+ * carries, not a parallel computation that can drift from it.
+ */
+export function runPackagedContentPhase(projectRoot, discoveredSkills, logger) {
+    const crawl = checkPackagedAgentInstructionFiles(projectRoot, discoveredSkills);
+    const phase = buildPackagedContentPhase(crawl);
+    if (phase.issues.length > 0) {
+        reportPackagedContentIssues(asValidationIssues(phase.issues), logger);
+    }
+    return phase;
+}
 /**
  * Run the in-process consistency check phase and record its outcome.
  *
@@ -606,8 +757,12 @@ async function verifyTopLevelCommand(options, command) {
         // answer used to be a different one: `consistency` crawled, while
         // `files-config-dests` and `packaged-content` read `skills.config` keys and
         // were therefore blind to every skill discovered by a glob.
+        // `'refuse'`: a verify over a population it could not see is the
+        // green-without-checking shape this command exists to refuse. The throw
+        // lands in the command's catch → `handleCommandError`, exit 2, with the
+        // crawl's own root-relative sentence.
         const discoveredSkills = inProcess.length > 0 && config?.skills
-            ? await discoverSkillsFromConfig(config.skills, projectRoot)
+            ? await discoverSkillsFromConfig(config.skills, projectRoot, 'refuse')
             : [];
         // Post-build files config check: verify all dest paths exist in built output
         if (inProcess.includes(FILES_CONFIG_DESTS)) {
@@ -626,18 +781,10 @@ async function verifyTopLevelCommand(options, command) {
         // than only logging them — a file that must not ship has to be visible in
         // `issueCounts`, or a CI consumer reads a clean report for a bundle carrying
         // one. Warnings do not fail the run; the exit code still comes from errors.
+        // The zero-bundle refusal is derived inside the builder and logged from the
+        // built phase, so stderr, the document and the exit code carry one list.
         if (inProcess.includes(PACKAGED_CONTENT)) {
-            const packagedIssues = checkPackagedAgentInstructionFiles(projectRoot, discoveredSkills);
-            if (packagedIssues.length > 0) {
-                reportPackagedContentIssues(packagedIssues, logger);
-            }
-            const packagedResult = {
-                name: PACKAGED_CONTENT,
-                status: calculateValidationStatus(packagedIssues),
-                issueCounts: countBySeverity(packagedIssues),
-                issues: packagedIssues.map(toPublishedIssue),
-            };
-            phaseResults.push(packagedResult);
+            phaseResults.push(runPackagedContentPhase(projectRoot, discoveredSkills, logger));
         }
         // Consistency check: cross-reference discovered skills vs package.json and plugin assignments
         if (inProcess.includes('consistency')) {

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package/dist/skill-resolution/packaging-config.d.ts

@@ -10,6 +10,7 @@
  * `vibe-agent-toolkit.config.yaml` contributes.
  */
 import type { DeclaredEvalSuite, SkillPackagingConfig } from '@vibe-agent-toolkit/agent-skills';
+import { type DiscoveryUnreadablePolicy } from '../commands/skills/skill-discovery.js';
 import { type loadConfig } from '../utils/config-loader.js';
 /** Clear the per-root discovery caches (call when fixtures mutate between in-process runs). */
 export declare function resetSkillDiscoveryCache(): void;
@@ -22,19 +23,62 @@ export declare function resetSkillDiscoveryCache(): void;
  * skill's eval suite is an answer key no matter whose bundle is being built.
  *
  * Memoized per config root so a run over N skills under one root pays for discovery
- * once, not N times. Returns `[]` when there is no governing config or no skills
- * section — wild mode, where there is no project to enumerate.
+ * once, not N times — and served from the SAME discovery {@link getDiscoveredSkillsByPath}
+ * ran for {@link resolveSkillPackagingConfig}, so one root is crawled once per run, not
+ * once per question, and a crawl that refuses answers both questions the same way.
+ * Returns `[]` when there is no governing config or no skills section — wild mode,
+ * where there is no project to enumerate.
+ *
+ * ⚠️ Swallows exactly one failure: a config that cannot be LOADED (`ConfigLoadError`),
+ * which the caller's own config resolution has already reported. A failed DISCOVERY is
+ * not that and propagates — see {@link resolveSkillPackagingConfig} for what it means.
+ * The old bare `catch` here treated the two alike, so a refused directory listing
+ * quietly became "this project declares no eval suites".
+ */
+export declare function resolveProjectDeclaredEvalSuites(skillPath: string, unreadable: DiscoveryUnreadablePolicy): Promise<DeclaredEvalSuite[]>;
+/**
+ * The config root's declared skills, as absolute SKILL.md path → declared name.
+ *
+ * One expansion of `skills.include` per root per run. A discovery that THROWS is
+ * not memoized — the next question re-asks the filesystem — and under `'refuse'`
+ * it throws whenever the crawl refuses a directory it cannot list
+ * (`DirectoryListingRefusedError` from `@vibe-agent-toolkit/utils/crawl`): the
+ * declared population is then unknown, and the caller decides whether that stops
+ * the command or degrades it. A caller that degrades passes `{ degrade }` and
+ * gets every skill the crawl COULD see, with the refusal handed to its handler
+ * — see `DiscoveryUnreadablePolicy`. Nothing here decides for them.
+ *
+ * ⚠️ The memo is per root, not per policy: the first question about a root
+ * decides how that root's refusals are handled for the rest of the run. Every
+ * command resets the memo at its start (`resetSkillDiscoveryCache`), and only
+ * `vat audit` degrades, so a run never mixes the two.
  */
-export declare function resolveProjectDeclaredEvalSuites(skillPath: string): Promise<DeclaredEvalSuite[]>;
-export declare function getDiscoveredSkillsByPath(skillsSection: NonNullable<ReturnType<typeof loadConfig>>['skills'], configRoot: string): Promise<Map<string, string>>;
+export declare function getDiscoveredSkillsByPath(skillsSection: NonNullable<ReturnType<typeof loadConfig>>['skills'], configRoot: string, unreadable: DiscoveryUnreadablePolicy): Promise<Map<string, string>>;
 /**
  * Resolve the merged packaging config for one SKILL.md by walking UP to its
  * nearest-ancestor config and matching the skill by absolute path. Returns the
  * FULL merge (`skills.defaults` + `skills.config[name]`, keeping
  * `validation.allow`). `null` when there is no governing config, no `skills`
  * section, or the skill is not declared (wild mode).
+ *
+ * 🚨 `null` means "no config governs this skill" and NOTHING else. Two failures
+ * propagate instead of being folded into it, because both mean the answer is
+ * unknown rather than "none":
+ *   - `ConfigLoadError` — the governing config exists and could not be loaded;
+ *   - `DirectoryListingRefusedError` — the config loaded, but expanding its
+ *     `skills.include` reached a directory the crawl could not list, so the
+ *     declared population (and whether this skill is in it) is unknown.
+ * The second used to be swallowed by a bare `catch { return null; }` around the
+ * discovery, with no stated reason. Under it, ONE `chmod 000` directory anywhere
+ * an include pattern reaches returned `null` for EVERY skill under the config:
+ * `vat audit` validated them all config-free, reported `success`, exited 0 and
+ * named the directory only under `--debug`. A caller that would rather degrade
+ * than stop passes `{ degrade }` — `vat audit` does, files a
+ * `SCAN_PATH_UNREADABLE` finding on the directory, and every skill the crawl
+ * could still see keeps its config; the rest say `'refuse'`, as the same
+ * refusal already stops `vat skills validate` and `vat skills build`.
  */
-export declare function resolveSkillPackagingConfig(skillPath: string): Promise<SkillPackagingConfig | null>;
+export declare function resolveSkillPackagingConfig(skillPath: string, unreadable: DiscoveryUnreadablePolicy): Promise<SkillPackagingConfig | null>;
 /**
  * Audit's display variant: keep `validation.severity`, drop `validation.allow`
  * (audit shows every finding, including ones an `allow` entry would suppress).