@intutic/cli 1.9.0 → 1.10.1

package/dist/commands/skill.js

@@ -5,13 +5,263 @@
  */
 import { existsSync } from 'node:fs';
 import * as fs from 'node:fs/promises';
-import { join } from 'node:path';
-import { spawn } from 'node:child_process';
+import { createHash } from 'node:crypto';
+import { dirname, join } from 'node:path';
+import { spawn, execFileSync } from 'node:child_process';
 import { log } from '../lib/logger.js';
+import { NOT_AUTHENTICATED } from '../lib/authMessages.js';
 import { loadCredentials, loadConfig } from '../config/store.js';
-import { resolveControlPlaneUrl } from '../config/paths.js';
+import { getIntuticDir, resolveControlPlaneUrl } from '../config/paths.js';
 import { createApiClient } from '../lib/api.js';
+import { scanSkillContent, SKILL_SCAN_PATTERNS, scanScriptContent, SCRIPT_SCAN_PATTERNS, detectScriptLanguage, MAX_SKILL_DIR_DEPTH, MAX_FILES_PER_SKILL, MAX_SCRIPT_SCAN_BYTES, } from '@intutic/shared-types';
+import { ciscoScannerOnPath, runCiscoScan, combineCiscoSarifRuns, } from '../lib/ciscoScanner.js';
 import pc from 'picocolors';
+/**
+ * Cap a skill's content to the same bound the control plane's
+ * `SkillFileReportSchema` enforces (`z.string().max(65536)`) before it ever
+ * leaves this machine — truncating client-side rather than letting an
+ * oversized file 400 the whole report. `content` is judged, then stripped
+ * before persistence server-side either way (see that schema's own doc
+ * comment); a truncated judge input is a weaker signal, never a stored
+ * artifact, so silent truncation here is the same tradeoff
+ * `mirrorAdoptionService.ts`'s own `capBytes` makes for judge prompt fields.
+ */
+const MAX_SKILL_CONTENT_TRANSPORT_CHARS = 65536;
+export function capContentForTransport(content) {
+    return content.length > MAX_SKILL_CONTENT_TRANSPORT_CHARS
+        ? content.slice(0, MAX_SKILL_CONTENT_TRANSPORT_CHARS)
+        : content;
+}
+/** Where bundled skill directories live, mirroring the conventions
+ *  `services/sync-daemon/src/agentReporter.ts`'s `collectSkills` already
+ *  uses for `.agents/skills`, plus Claude Code's own `.claude/skills`. Each
+ *  entry directly under the root is a skill; `SKILL.md` is its content. */
+const SKILL_DIRECTORY_ROOTS = [
+    { dir: '.agents/skills', source: '.agents/skills' },
+    { dir: '.claude/skills', source: '.claude/skills' },
+];
+/**
+ * Read, content-scan, and (if `prune` is set and the scan is not clean)
+ * auto-prune one real skill file. Extracted from `runSkillAudit` so the
+ * discovery/read/scan/report path is testable without the network and
+ * credentials setup the full command does.
+ *
+ * Refusal-not-pass: a read failure returns `scanned: false` with
+ * `issuesDetected: 0` — the zero is not a clean bill of health, it is "we
+ * never got to look." Callers must treat `scanned: false` as its own status,
+ * never as `clean`.
+ */
+export async function auditSkillFile(filePath, fullPath, prune, 
+/** Suppresses the per-finding `log.warn` narrative. Used by `--sarif`
+ *  (`runSkillAudit`), whose stdout contract is a single JSON document — a
+ *  CI tool piping that into a SARIF parser must not see decorated text
+ *  interleaved with it. Findings are still returned; only the console
+ *  narration is skipped. Defaults to `false` so every existing caller
+ *  (including the tests that assert on `log.warn` output indirectly via
+ *  behaviour) is unaffected. */
+quiet = false, 
+/**
+ * Phase S5 (TD-357). Attach the file's full content to the returned entry
+ * — only ever set by a caller that already confirmed
+ * `semanticSkillAnalysisEnabled` for this workspace (`runSkillAudit`
+ * below reads it off `client.fetchConfig`'s resolved settings, the same
+ * way it already reads `enableLocalSkillAuditDelete`). Defaults to
+ * `false` so every existing caller/test is unaffected. */
+attachContent = false) {
+    let content;
+    try {
+        content = await fs.readFile(fullPath, 'utf8');
+    }
+    catch (err) {
+        if (!quiet) {
+            log.warn(`[${filePath}] Could not be read (${err instanceof Error ? err.message : String(err)}) — reported as unscanned, not clean.`);
+        }
+        return { filePath, linesCount: 0, issuesDetected: 0, scanned: false, kind: 'skill_md' };
+    }
+    const contentLines = content.split('\n');
+    const result = scanSkillContent(content);
+    const sha256 = createHash('sha256').update(content, 'utf8').digest('hex');
+    if (!result.clean && !quiet) {
+        for (const finding of result.findings) {
+            log.warn(`[${filePath}] ${finding.category} finding (${finding.patternId})${finding.excerpt ? `: ${finding.excerpt}` : ''}`);
+        }
+    }
+    // Auto-prune worthy findings, same opt-in as the legacy rule-file audit:
+    // drop any LINE that itself trips a pattern, line-by-line — mirroring the
+    // existing per-line re-scan below rather than deleting the whole file,
+    // since a skill missing a few flagged lines still functions.
+    if (!result.clean && prune) {
+        let fileUpdated = false;
+        const filteredLines = contentLines.filter((line) => {
+            if (!scanSkillContent(line).clean) {
+                fileUpdated = true;
+                return false;
+            }
+            return true;
+        });
+        if (fileUpdated) {
+            await fs.writeFile(fullPath, filteredLines.join('\n'), 'utf8');
+            if (!quiet)
+                log.success(`[${filePath}] Auto-pruned lines flagged by the skill-content scan.`);
+        }
+    }
+    return {
+        filePath,
+        linesCount: contentLines.length,
+        issuesDetected: result.findings.length,
+        findings: result.findings,
+        sha256,
+        scanned: true,
+        kind: 'skill_md',
+        ...(attachContent ? { content: capContentForTransport(content) } : {}),
+    };
+}
+/** Enumerate real `SKILL.md` files under both skill directory roots. A
+ *  missing root is not an error — most workspaces have neither. Exported so
+ *  tests can walk a fixture directory tree without going through the full
+ *  `skill audit`/`skill list` command (credentials, network, etc). */
+export async function discoverSkillFiles(workspaceRoot) {
+    const out = [];
+    for (const root of SKILL_DIRECTORY_ROOTS) {
+        const dir = join(workspaceRoot, root.dir);
+        let entries;
+        try {
+            entries = await fs.readdir(dir, { withFileTypes: true });
+        }
+        catch {
+            continue;
+        }
+        for (const entry of entries) {
+            if (!entry.isDirectory())
+                continue;
+            const filePath = join(root.dir, entry.name, 'SKILL.md');
+            const fullPath = join(workspaceRoot, filePath);
+            if (existsSync(fullPath)) {
+                out.push({ filePath, fullPath, source: root.source });
+            }
+        }
+    }
+    return out;
+}
+/**
+ * Bounded, symlink-skipping recursive walk of a skill directory's sibling
+ * files — everything alongside `SKILL.md`, the surface TD-356
+ * (`docs/TECH_DEBT.md`) named as unenumerated. `SKILL.md` itself is excluded
+ * (it is already covered by `discoverSkillFiles`/`auditSkillFile` above);
+ * everything else found, at any depth up to the cap, is a candidate for
+ * `auditScriptFile`.
+ *
+ * Bounded by `MAX_SKILL_DIR_DEPTH` and `MAX_FILES_PER_SKILL`
+ * (`@intutic/shared-types`) — a skill directory is developer-authored
+ * content, not something this command should ever walk unboundedly. Depth 0
+ * is the skill directory itself; nested subdirectories increment from
+ * there, and the walk stops recursing once depth exceeds the cap.
+ *
+ * Symlinks are never followed: `Dirent.isSymbolicLink()` is checked during
+ * `readdir` and skipped outright, without ever stat-ing or resolving where
+ * the link points. A symlink inside a skill directory could point outside
+ * that directory — or outside the workspace entirely — which would turn a
+ * bounded, skill-scoped walk into an effectively unbounded one, and would
+ * let a skill directory "bundle" a script that does not actually live on
+ * disk inside it.
+ */
+export async function discoverSkillBundledFiles(workspaceRoot, 
+/** Path to the skill directory (not `SKILL.md` itself), relative to
+ *  `workspaceRoot`, e.g. `.agents/skills/my-skill`. */
+skillDirPath) {
+    const out = [];
+    async function walk(relDir, depth) {
+        if (depth > MAX_SKILL_DIR_DEPTH || out.length >= MAX_FILES_PER_SKILL)
+            return;
+        let entries;
+        try {
+            entries = await fs.readdir(join(workspaceRoot, relDir), { withFileTypes: true });
+        }
+        catch {
+            return;
+        }
+        for (const entry of entries) {
+            if (out.length >= MAX_FILES_PER_SKILL)
+                return;
+            if (entry.isSymbolicLink())
+                continue; // never follow — see doc comment above
+            const relPath = join(relDir, entry.name);
+            if (entry.isDirectory()) {
+                await walk(relPath, depth + 1);
+            }
+            else if (entry.isFile()) {
+                if (depth === 0 && entry.name === 'SKILL.md')
+                    continue;
+                out.push({ filePath: relPath, fullPath: join(workspaceRoot, relPath) });
+            }
+        }
+    }
+    await walk(skillDirPath, 0);
+    return out;
+}
+/**
+ * Read, hash, and — when recognized and within the byte cap — content-scan
+ * one bundled script file discovered by `discoverSkillBundledFiles`.
+ *
+ * The sha256 hash is ALWAYS computed, even for a file this scanner cannot
+ * itself interpret (a binary, an unrecognized extension with no useful
+ * shebang) — that is deliberate, not a leftover from a simpler version of
+ * this function. A later, separate, opt-in phase (Cisco `skill-scanner` /
+ * VirusTotal-style hash lookup, Phase S3) needs the hash of every bundled
+ * file regardless of whether THIS scanner's regex patterns can say anything
+ * about its content.
+ *
+ * Refusal-not-pass, same contract as `auditSkillFile`: a read failure, a
+ * file over `MAX_SCRIPT_SCAN_BYTES`, or an unrecognized language all return
+ * `scanned: false` — never folded into `issuesDetected: 0` implying safety.
+ * A file over the byte cap is a REFUSAL to look, reported as such, not a
+ * silent skip and not a false "clean".
+ */
+export async function auditScriptFile(filePath, fullPath, quiet = false) {
+    let buffer;
+    try {
+        buffer = await fs.readFile(fullPath);
+    }
+    catch (err) {
+        if (!quiet) {
+            log.warn(`[${filePath}] Could not be read (${err instanceof Error ? err.message : String(err)}) — reported as unscanned, not clean.`);
+        }
+        return { filePath, linesCount: 0, issuesDetected: 0, scanned: false, kind: 'script' };
+    }
+    const sha256 = createHash('sha256').update(buffer).digest('hex');
+    const firstLine = buffer.toString('utf8', 0, Math.min(buffer.length, 200)).split('\n')[0];
+    const language = detectScriptLanguage(filePath, firstLine);
+    if (buffer.length > MAX_SCRIPT_SCAN_BYTES) {
+        if (!quiet) {
+            log.warn(`[${filePath}] Exceeds the ${MAX_SCRIPT_SCAN_BYTES}-byte script scan cap — refusing to scan (hash recorded).`);
+        }
+        return { filePath, linesCount: 0, issuesDetected: 0, sha256, scanned: false, kind: 'script', language };
+    }
+    if (language === 'unknown') {
+        // Not a script language this scanner understands (binary, data file,
+        // unrecognized extension with no useful shebang) — hash-only, same
+        // refusal-not-pass status as an over-cap file.
+        return { filePath, linesCount: 0, issuesDetected: 0, sha256, scanned: false, kind: 'script', language };
+    }
+    const content = buffer.toString('utf8');
+    const contentLines = content.split('\n');
+    const result = scanScriptContent(content, language);
+    if (!result.clean && !quiet) {
+        for (const finding of result.findings) {
+            log.warn(`[${filePath}] ${finding.category} finding (${finding.patternId})${finding.excerpt ? `: ${finding.excerpt}` : ''}`);
+        }
+    }
+    return {
+        filePath,
+        linesCount: contentLines.length,
+        issuesDetected: result.findings.length,
+        findings: result.findings,
+        sha256,
+        scanned: true,
+        kind: 'script',
+        language,
+    };
+}
 // ─── Skill Commands ──────────────────────────────────────────────────
 export async function runSkillList() {
     log.header('Intutic — Skill Discovery');
@@ -40,6 +290,23 @@ export async function runSkillList() {
             });
         }
     }
+    // Real skill directories (`.agents/skills`, `.claude/skills`) — discovery
+    // only here, matching the existing "list only counts" contract for this
+    // command; content scanning happens in `skill audit` below.
+    const skillFiles = await discoverSkillFiles(workspaceRoot);
+    for (const { filePath } of skillFiles) {
+        found++;
+        let lines = 0;
+        try {
+            lines = (await fs.readFile(join(workspaceRoot, filePath), 'utf8')).split('\n').length;
+        }
+        catch {
+            // Discovery already found the directory entry; a read failure here
+            // just means we can't report a line count.
+        }
+        console.log(`  ${pc.green('✔')} ${pc.bold(filePath)} (${lines} lines)`);
+        skillsReport.push({ filePath, linesCount: lines, issuesDetected: 0 });
+    }
     if (found === 0) {
         log.info('No active skill or rule files found in workspace root.');
     }
@@ -54,28 +321,252 @@ export async function runSkillList() {
             await client.post(`/api/v1/workspaces/${creds.workspaceId}/skills/report`, { skills: skillsReport });
             log.dim('Reported local skills to Intutic control plane.');
         }
-        catch (err) {
-            // Non-blocking
+        catch {
+            // Non-blocking: discovery already printed everything the user asked for,
+            // and the report is a convenience for the dashboard.
+        }
+    }
+}
+/**
+ * A minimal, valid SARIF 2.1.0 document for CI/code-scanning interop.
+ *
+ * Built for GitHub Code Scanning and any other consumer of the format — not
+ * for Cisco's open-source `skill-scanner` project specifically, but so that
+ * tool's findings and ours can land in the same code-scanning pane on a repo
+ * that runs both. We do not shell out to or depend on that project; this is
+ * only a compatible OUTPUT shape.
+ *
+ * `rules` lists every pattern `scanSkillContent` knows how to report —
+ * SARIF's convention is the tool's full rule catalog, not only the ids that
+ * fired in this run, so a code-scanning UI can show a rule as "0 findings"
+ * rather than "unknown rule". `results` is built only from real skill files
+ * (`SkillReportEntry.findings`, populated by `auditSkillFile`); the legacy
+ * `.cursorrules`/`CLAUDE.md` regex checks above have no pattern ids and stay
+ * out of SARIF for that reason — see the entries' own `findings` being
+ * absent, not an omission here.
+ *
+ * `locations` deliberately carries no `region`: `SkillScanFinding` bounds an
+ * excerpt (see `skillScan.ts`'s `excerptFor`) but not a line/column, and
+ * SARIF's `region` is optional — fabricating `startLine: 1` would claim a
+ * precision this scanner does not have.
+ *
+ * `additionalRuns` (Phase S3): zero or more extra SARIF `runs[]`-shaped
+ * objects appended AFTER this codebase's own run — the Cisco skill-scanner
+ * integration's combined run, when that engine ran. SARIF is explicitly
+ * designed to carry multiple runs from different tools in one document, so
+ * these are appended AS-IS, never translated or merged into this function's
+ * own `results`/`rules` — that translation only happens for the internal
+ * `SkillScanFinding` representation (`mergeCiscoFindings`), never for this
+ * output mode.
+ */
+export function buildSarifLog(entries, additionalRuns = []) {
+    const results = entries.flatMap((entry) => (entry.findings ?? []).map((finding) => ({
+        ruleId: finding.patternId,
+        level: 'warning',
+        message: {
+            text: finding.excerpt
+                ? `${finding.category} finding: ${finding.excerpt}`
+                : `${finding.category} finding (${finding.patternId})`,
+        },
+        locations: [
+            {
+                physicalLocation: {
+                    artifactLocation: { uri: entry.filePath },
+                },
+            },
+        ],
+    })));
+    return {
+        $schema: 'https://raw.githubusercontent.com/oasis-tcs/sarif-spec/master/Schemata/sarif-schema-2.1.0.json',
+        version: '2.1.0',
+        runs: [
+            {
+                tool: {
+                    driver: {
+                        name: 'intutic-skill-scan',
+                        informationUri: 'https://intutic.ai',
+                        // The rule catalog is the union of both pattern tables — SARIF's
+                        // convention is one driver's full rule set, not just the ids
+                        // that fired this run, so a code-scanning UI can show a rule as
+                        // "0 findings" rather than "unknown rule". Bundled-script
+                        // findings (Phase S2, `SCRIPT_SCAN_PATTERNS`) land in the same
+                        // `intutic-skill-scan` driver as `SKILL.md` content findings —
+                        // one driver name, not a second tool, since both are the same
+                        // "scan agent-loaded content for these threat shapes" capability.
+                        rules: [...SKILL_SCAN_PATTERNS, ...SCRIPT_SCAN_PATTERNS].map((pattern) => ({
+                            id: pattern.id,
+                            shortDescription: { text: pattern.description },
+                            defaultConfiguration: { level: 'warning' },
+                            properties: { category: pattern.category },
+                        })),
+                    },
+                },
+                // Present and empty, never omitted, when nothing was flagged — a
+                // missing `results` key reads to some SARIF consumers as "the tool
+                // did not run" rather than "the tool ran and found nothing".
+                results,
+            },
+            ...additionalRuns,
+        ],
+    };
+}
+/**
+ * Longest excerpt a Cisco finding's `message` is trimmed to before becoming
+ * a `SkillScanFinding.excerpt`. Matches the control plane's
+ * `SkillScanFindingSchema.excerpt` cap (`harnessConfig.ts`) — this codebase's
+ * own findings bound their excerpt to ~40 chars of surrounding context
+ * (`EXCERPT_RADIUS`, `skillScan.ts`), but a Cisco `message.text` is a full
+ * LLM-authored sentence, not a regex match window, so this cap is generous
+ * rather than matching that radius — it exists to reject an attempt to
+ * smuggle something much larger through this field, not to enforce a tight
+ * budget on a legitimate finding description.
+ */
+const CISCO_EXCERPT_CAP = 2000;
+/**
+ * Maps the real `skill-scanner` category taxonomy — the `ThreatCategory`
+ * enum in the installed 2.0.13 package's `skill_scanner/core/models.py`,
+ * carried on each SARIF result's `properties.category` (see
+ * `lib/ciscoScanner.ts`'s module doc comment for how it's extracted) — onto
+ * this codebase's own three-category taxonomy. `prompt_injection` covers
+ * deception/manipulation vectors (including ones aimed at a human or the
+ * discovery/trust mechanism itself, not just the model); `data_exfiltration`
+ * covers anything about data or credentials leaving; everything else
+ * (execution, abuse, supply-chain, or genuinely uncategorizable) falls back
+ * to `'malicious_code'`, the broadest of the three buckets.
+ */
+const CISCO_CATEGORY_MAP = {
+    prompt_injection: 'prompt_injection',
+    social_engineering: 'prompt_injection',
+    harmful_content: 'prompt_injection',
+    skill_discovery_abuse: 'prompt_injection',
+    transitive_trust_abuse: 'prompt_injection',
+    unicode_steganography: 'prompt_injection',
+    data_exfiltration: 'data_exfiltration',
+    hardcoded_secrets: 'data_exfiltration',
+    command_injection: 'malicious_code',
+    unauthorized_tool_use: 'malicious_code',
+    obfuscation: 'malicious_code',
+    resource_abuse: 'malicious_code',
+    policy_violation: 'malicious_code',
+    malware: 'malicious_code',
+    autonomy_abuse: 'malicious_code',
+    tool_chaining_abuse: 'malicious_code',
+    supply_chain_attack: 'malicious_code',
+};
+/** See {@link CISCO_CATEGORY_MAP}. Exported for tests. */
+export function mapCiscoCategory(category) {
+    if (!category)
+        return 'malicious_code';
+    return CISCO_CATEGORY_MAP[category] ?? 'malicious_code';
+}
+/**
+ * Merges one skill directory's Cisco findings into that skill's existing
+ * report entries — the `SKILL.md` row, or a bundled-script row when a
+ * finding's own location matches one of `candidateEntries` exactly. Falls
+ * back to `fallbackEntry` (always the skill's `SKILL.md` row) when no
+ * location match is found — this codebase does not assume `skill-scanner`
+ * always attributes a finding to a specific bundled file, so an
+ * unmatched/absent location is treated as "belongs to the skill as a
+ * whole," not an error.
+ *
+ * Each Cisco finding becomes a `SkillScanFinding` with `patternId: 'cisco.'
+ * + ruleId`, a category from {@link mapCiscoCategory} (mapped from the
+ * finding's own `category`, not its `ruleId`), an excerpt capped at
+ * {@link CISCO_EXCERPT_CAP}, and `engine: 'cisco-skill-scanner'` — this
+ * codebase's own findings stamp `engine: 'native'` at construction
+ * (`skillScan.ts`/`scriptScan.ts`), so every finding in a report entry now
+ * carries its provenance.
+ *
+ * Returns the number of findings merged, for the caller's running `issues`
+ * count.
+ */
+export function mergeCiscoFindings(candidateEntries, fallbackEntry, ciscoResult, workspaceRoot) {
+    if (!ciscoResult.ok)
+        return 0;
+    for (const finding of ciscoResult.findings) {
+        const mapped = {
+            patternId: `cisco.${finding.ruleId}`,
+            category: mapCiscoCategory(finding.category),
+            excerpt: finding.message.slice(0, CISCO_EXCERPT_CAP) || undefined,
+            engine: 'cisco-skill-scanner',
+        };
+        let target;
+        if (finding.filePath) {
+            const relPath = finding.filePath.startsWith(workspaceRoot)
+                ? finding.filePath.slice(workspaceRoot.length).replace(/^[/\\]/, '')
+                : finding.filePath;
+            target = candidateEntries.find((e) => e.filePath === relPath);
         }
+        target ??= fallbackEntry;
+        target.findings = [...(target.findings ?? []), mapped];
+        target.issuesDetected += 1;
     }
+    return ciscoResult.findings.length;
 }
-export async function runSkillAudit() {
-    log.header('Intutic — Skill Security Audit');
+export async function runSkillAudit(opts = {}) {
+    const sarif = opts.sarif === true;
+    // SARIF's contract is a single JSON document on stdout — a CI tool piping
+    // this into a code-scanning upload must not see decorated progress text
+    // interleaved with it. Every narrative call below is gated on `!sarif`;
+    // findings are still collected and reported identically either way.
+    if (!sarif)
+        log.header('Intutic — Skill Security Audit');
     const config = loadConfig();
     const workspaceRoot = config?.workspaceRoot ?? process.cwd();
     const creds = await loadCredentials().catch(() => null);
     let enableLocalSkillAuditDelete = false;
-    // Fetch workspace settings to see if auto-delete is enabled
+    let ciscoSkillScannerEnabled = false;
+    // Phase S5 (TD-357): gates whether `auditSkillFile` below attaches full
+    // `SKILL.md` content to its report entry. Off unless the workspace opted
+    // in — see `WorkspaceSettings.semanticSkillAnalysisEnabled`'s own doc
+    // comment for what turning it on transmits.
+    let semanticSkillAnalysisEnabled = false;
+    // Fetch workspace settings to see if auto-delete / the Cisco auto-run /
+    // semantic analysis are enabled
     if (creds) {
         try {
             const client = await getClient(config?.devMode);
             const syncConfig = await client.fetchConfig(creds.workspaceId);
             enableLocalSkillAuditDelete = syncConfig.settings?.enableLocalSkillAuditDelete ?? false;
+            ciscoSkillScannerEnabled = syncConfig.settings?.ciscoSkillScannerEnabled ?? false;
+            semanticSkillAnalysisEnabled = syncConfig.settings?.semanticSkillAnalysisEnabled ?? false;
         }
         catch {
             // fallback to false
         }
     }
+    // ── Cisco skill-scanner engine resolution (Phase S3) ──────────────────
+    //
+    // Native scanning always runs — it is this command's baseline and always
+    // available. The Cisco engine additionally runs when EITHER:
+    //   - `--engine cisco` was explicitly passed: a LOUD failure (non-zero
+    //     exit) if the binary is absent, since the user explicitly asked for
+    //     this engine and a silent skip would look like a clean scan.
+    //   - the `ciscoSkillScannerEnabled` workspace setting is on: a graceful,
+    //     info-level skip if the binary is absent, since this is an opt-in
+    //     AUTO-run path, not an explicit request.
+    if (opts.engine !== undefined && opts.engine !== 'native' && opts.engine !== 'cisco') {
+        log.error(`Unknown --engine value '${opts.engine}'. Expected 'native' or 'cisco'.`);
+        process.exit(1);
+    }
+    const requestedCisco = opts.engine === 'cisco';
+    let runCisco = false;
+    if (requestedCisco || ciscoSkillScannerEnabled) {
+        const available = await ciscoScannerOnPath();
+        if (available) {
+            runCisco = true;
+        }
+        else if (requestedCisco) {
+            log.error("Cisco skill-scanner engine requested (--engine cisco) but the 'skill-scanner' binary " +
+                'is not on PATH. Install it with `pipx install cisco-ai-skill-scanner`.');
+            process.exit(1);
+        }
+        else if (!sarif) {
+            log.info("ciscoSkillScannerEnabled is on, but the 'skill-scanner' binary is not on PATH — " +
+                'skipping the Cisco engine for this run (native scanning still ran).');
+        }
+    }
+    const ciscoRawSarifRuns = [];
     const filesToScan = [
         '.cursorrules',
         'CLAUDE.md',
@@ -89,31 +580,35 @@ export async function runSkillAudit() {
         if (existsSync(fullPath)) {
             const content = await fs.readFile(fullPath, 'utf8');
             let fileIssues = 0;
-            let contentLines = content.split('\n');
+            const contentLines = content.split('\n');
             let fileUpdated = false;
             // 1. Audit for secrets (AWS, Intutic, generic keys)
             if (content.match(/vk_[a-zA-Z0-9]{30,}/)) {
-                log.error(`[${file}] Hardcoded Intutic virtual key prefix detected.`);
+                if (!sarif)
+                    log.error(`[${file}] Hardcoded Intutic virtual key prefix detected.`);
                 fileIssues++;
             }
             if (content.match(/sk-live-[a-zA-Z0-9]{30,}/)) {
-                log.error(`[${file}] Hardcoded API secrets detected.`);
+                if (!sarif)
+                    log.error(`[${file}] Hardcoded API secrets detected.`);
                 fileIssues++;
             }
             // 2. Audit for unsafe wildcard commands (e.g. rm -rf *, sh *)
-            if (content.match(/rm\s+-rf\s+[\*\/]/)) {
-                log.warn(`[${file}] Unsafe recursive delete wildcard patterns (rm -rf *) found.`);
+            if (content.match(/rm\s+-rf\s+[*/]/)) {
+                if (!sarif)
+                    log.warn(`[${file}] Unsafe recursive delete wildcard patterns (rm -rf *) found.`);
                 fileIssues++;
             }
             if (content.match(/curl\s+|wget\s+/)) {
-                log.warn(`[${file}] Network retrieval commands (curl, wget) found inside rules instructions.`);
+                if (!sarif)
+                    log.warn(`[${file}] Network retrieval commands (curl, wget) found inside rules instructions.`);
                 fileIssues++;
             }
             // 3. Auto-delete/prune unsafe lines if setting is enabled
             if (fileIssues > 0 && enableLocalSkillAuditDelete) {
                 const filteredLines = contentLines.filter((line) => {
                     const isSecret = line.match(/vk_[a-zA-Z0-9]{30,}/) || line.match(/sk-live-[a-zA-Z0-9]{30,}/);
-                    const isUnsafeCmd = line.match(/rm\s+-rf\s+[\*\/]/) || line.match(/curl\s+|wget\s+/);
+                    const isUnsafeCmd = line.match(/rm\s+-rf\s+[*/]/) || line.match(/curl\s+|wget\s+/);
                     if (isSecret || isUnsafeCmd) {
                         fileUpdated = true;
                         return false;
@@ -122,7 +617,8 @@ export async function runSkillAudit() {
                 });
                 if (fileUpdated) {
                     await fs.writeFile(fullPath, filteredLines.join('\n'), 'utf8');
-                    log.success(`[${file}] Auto-pruned unsafe lines/rules during security audit.`);
+                    if (!sarif)
+                        log.success(`[${file}] Auto-pruned unsafe lines/rules during security audit.`);
                 }
             }
             issues += fileIssues;
@@ -133,7 +629,60 @@ export async function runSkillAudit() {
             });
         }
     }
-    if (issues === 0) {
+    // ── Real skill directories (`.agents/skills`, `.claude/skills`) ──────
+    //
+    // Content-aware scan via `scanSkillContent` (`@intutic/shared-types`),
+    // report-only per that module's doc comment — a finding here is never
+    // treated as ground truth, only surfaced. `enableLocalSkillAuditDelete`
+    // gates pruning here exactly as it already gates the legacy rule-file
+    // pruning above: the same opt-in, now covering both audit paths.
+    const skillFiles = await discoverSkillFiles(workspaceRoot);
+    for (const { filePath, fullPath } of skillFiles) {
+        const entry = await auditSkillFile(filePath, fullPath, enableLocalSkillAuditDelete, sarif, semanticSkillAnalysisEnabled);
+        issues += entry.issuesDetected;
+        skillsReport.push(entry);
+        // ── Bundled scripts alongside this skill's SKILL.md (TD-356, Phase S2) ─
+        //
+        // `discoverSkillFiles` only ever found `SKILL.md`; a sibling `setup.sh`
+        // or `helper.py` was invisible to every consumer before this. Enumerate
+        // (bounded, symlink-skipping — see `discoverSkillBundledFiles`) and
+        // audit each one the same way: always hashed, content-scanned only when
+        // the language is recognized and the file is within the byte cap.
+        const skillDirPath = dirname(filePath);
+        const bundledFiles = await discoverSkillBundledFiles(workspaceRoot, skillDirPath);
+        const bundledEntries = [];
+        for (const script of bundledFiles) {
+            const scriptEntry = await auditScriptFile(script.filePath, script.fullPath, sarif);
+            issues += scriptEntry.issuesDetected;
+            skillsReport.push(scriptEntry);
+            bundledEntries.push(scriptEntry);
+        }
+        // ── Cisco skill-scanner engine (Phase S3, opt-in) ───────────────────
+        //
+        // One invocation per skill directory — see `lib/ciscoScanner.ts`'s
+        // module doc comment for why the real CLI cannot take more than one
+        // `--path` per invocation. Findings merge into this skill's existing
+        // entries (SKILL.md or a matching bundled-script row); the raw SARIF
+        // run is kept separately for verbatim passthrough below.
+        if (runCisco) {
+            const [ciscoResult] = await runCiscoScan([join(workspaceRoot, skillDirPath)]);
+            if (ciscoResult.ok) {
+                issues += mergeCiscoFindings([entry, ...bundledEntries], entry, ciscoResult, workspaceRoot);
+                ciscoRawSarifRuns.push(...ciscoResult.sarifRuns);
+            }
+            else if (!sarif) {
+                log.warn(`[cisco] ${skillDirPath}: ${ciscoResult.error}`);
+            }
+        }
+    }
+    if (sarif) {
+        // The whole point: one JSON document, nothing else, on stdout. Cisco's
+        // combined run (if the engine ran) appends as a second `runs[]` entry,
+        // verbatim — see `buildSarifLog`'s doc comment.
+        const combinedCiscoRun = combineCiscoSarifRuns(ciscoRawSarifRuns);
+        console.log(JSON.stringify(buildSarifLog(skillsReport, combinedCiscoRun ? [combinedCiscoRun] : []), null, 2));
+    }
+    else if (issues === 0) {
         log.success('Skill security audit passed. No credentials or critical safety risks detected.');
     }
     else {
@@ -150,14 +699,109 @@ export async function runSkillAudit() {
         }
     }
 }
+/**
+ * Lists staged files under the skill surface (`.agents/skills/**`,
+ * `.claude/skills/**`), ADDED/COPIED/MODIFIED only — mirroring the secret
+ * pre-commit scan's `git diff --cached` scope in `lib/gitHooks.ts`, so both
+ * checks agree on what "staged" means. A deleted skill file has nothing to
+ * scan.
+ *
+ * `execFileSync`, matching this package's existing git-invocation
+ * convention (`config/keychain.ts`, `commands/install-daemon.ts`) rather
+ * than a shelled-out string — no quoting to get wrong.
+ */
+function listStagedSkillSurfaceFiles(workspaceRoot) {
+    try {
+        const out = execFileSync('git', ['diff', '--cached', '--name-only', '--diff-filter=ACM', '--', '.agents/skills', '.claude/skills'], { cwd: workspaceRoot, encoding: 'utf8' });
+        return out.split('\n').map((l) => l.trim()).filter(Boolean);
+    }
+    catch {
+        // Not a git repo, no staged changes, or git not on PATH — nothing to scan.
+        return [];
+    }
+}
+/**
+ * Reads the STAGED content of a path via `git show :<path>` — the blob that
+ * will actually be committed, not whatever is currently on disk. A file
+ * edited again after `git add` would otherwise be scanned in a state that
+ * does not match what `git commit` is about to record.
+ */
+function readStagedBlob(workspaceRoot, filePath) {
+    try {
+        return execFileSync('git', ['show', `:${filePath}`], { cwd: workspaceRoot, encoding: 'utf8' });
+    }
+    catch {
+        return null;
+    }
+}
+/**
+ * Warn-only skill-content scan over staged additions in the skill surface.
+ *
+ * TD-358. This is the CLI entry point `lib/gitHooks.ts`'s pre-commit hook
+ * shells out to (`intutic skill scan-staged`) — deliberately separate from
+ * `skill audit` above, which scans the whole workspace and is too slow and
+ * too broad for a commit-time check that must stay fast.
+ *
+ * Never refuses a commit and never throws: `scanSkillContent`'s
+ * false-positive rate against real, benign skill markdown is unmeasured (see
+ * `skillScan.ts`'s module doc comment), so this phase stages the signal as
+ * an advisory only. Contrast `lib/gitHooks.ts`'s secret scan, which DOES
+ * refuse — that check is high-precision, prefixed credential shapes with no
+ * known false positives; this one is not, and must not borrow that check's
+ * authority until it has earned it the same way.
+ */
+export async function runSkillScanStaged() {
+    const config = loadConfig();
+    const workspaceRoot = config?.workspaceRoot ?? process.cwd();
+    const staged = listStagedSkillSurfaceFiles(workspaceRoot);
+    if (staged.length === 0)
+        return;
+    let flaggedFiles = 0;
+    for (const filePath of staged) {
+        const content = readStagedBlob(workspaceRoot, filePath);
+        if (content === null)
+            continue; // vanished between diff and show — nothing to scan
+        const result = scanSkillContent(content);
+        if (result.clean)
+            continue;
+        flaggedFiles++;
+        for (const finding of result.findings) {
+            log.warn(`[${filePath}] ${finding.category} finding (${finding.patternId})` +
+                `${finding.excerpt ? `: ${finding.excerpt}` : ''} — advisory only, not blocking this commit.`);
+        }
+    }
+    if (flaggedFiles > 0) {
+        log.warn(`Skill-content scan flagged ${flaggedFiles} staged file(s) under .agents/skills or ` +
+            '.claude/skills. This is advisory only (TD-358) — the commit proceeds. Run ' +
+            '`intutic skill audit` for the full report.');
+    }
+    // No exit code is ever set here — the caller (the pre-commit hook) always
+    // treats this check as successful, by construction.
+}
 // ─── Loop Commands ───────────────────────────────────────────────────
-async function getClient(dev) {
+// Exported so `commands/decision.ts` can share the exact same client
+// resolution (creds, dev-mode precedence, base URL) rather than growing a
+// second, easily-drifting copy of it.
+export async function getClient(dev) {
     const creds = await loadCredentials();
     if (!creds) {
-        log.error('Not authenticated. This command needs an Intutic control plane, which open core does not include. To run the proxy without one: `intutic start`.');
+        log.error(NOT_AUTHENTICATED);
         process.exit(1);
     }
-    const devMode = dev || process.env.INTUTIC_DEV === '1';
+    // `config?.devMode` is load-bearing and was missing here.
+    //
+    // Every other command that talks to the control plane resolves dev mode as
+    // `flag || config.devMode || INTUTIC_DEV` (sops, policy, budget, connect, exec).
+    // This one read only the flag and the env var, so a workspace configured with
+    // `devMode: true` still had `intutic loop start` resolve to https://api.intutic.ai
+    // — the loop commands, which are the governance feature, were the one family that
+    // ignored the workspace's own setting and silently addressed production.
+    //
+    // It went unnoticed because tools/cli/dist was stale: the built CLI predated this
+    // code and still read the config, so the bug only appeared once a workspace build
+    // regenerated dist from source.
+    const config = loadConfig();
+    const devMode = dev || config?.devMode || process.env.INTUTIC_DEV === '1';
     const controlPlaneUrl = resolveControlPlaneUrl(devMode);
     return createApiClient(controlPlaneUrl, creds.apiKey);
 }
@@ -167,7 +811,7 @@ async function resolveLocalSops(sopsArg) {
     const config = loadConfig();
     const workspaceRoot = config?.workspaceRoot ?? process.cwd();
     const sopsDir = join(workspaceRoot, '.intutic', 'sops');
-    let dirs = [];
+    let dirs;
     try {
         const entries = await fs.readdir(sopsDir, { withFileTypes: true });
         dirs = entries.filter((e) => e.isDirectory()).map((e) => e.name);
@@ -220,14 +864,14 @@ export async function runLoopStart(opts) {
             log.success(`Loop run active: ${pc.bold(res.loop.loopRunId)}`);
             log.info(`Budget limit: $${res.loop.budgetLimitUsd} USD`);
             // Write loop env file locally
-            const loopEnvPath = join(process.env.HOME || '', '.intutic', 'env', 'loop.env');
+            const loopEnvPath = join(getIntuticDir(), 'env', 'loop.env');
             await fs.mkdir(dirname(loopEnvPath), { recursive: true }).catch(() => { });
             await fs.writeFile(loopEnvPath, `INTUTIC_LOOP_RUN_ID=${res.loop.loopRunId}\n`);
             log.dim(`Wrote run context to ~/.intutic/env/loop.env`);
         }
     }
     catch (err) {
-        log.error(`Failed to register loop: ${err.message}`);
+        log.error(`Failed to register loop: ${err instanceof Error ? err.message : String(err)}`);
     }
 }
 export async function runLoopComplete(loopRunId, opts) {
@@ -238,12 +882,12 @@ export async function runLoopComplete(loopRunId, opts) {
         if (res.ok) {
             log.success(`Loop run ${loopRunId} completed.`);
             // Clean env
-            const loopEnvPath = join(process.env.HOME || '', '.intutic', 'env', 'loop.env');
+            const loopEnvPath = join(getIntuticDir(), 'env', 'loop.env');
             await fs.rm(loopEnvPath, { force: true });
         }
     }
     catch (err) {
-        log.error(`Failed to complete loop: ${err.message}`);
+        log.error(`Failed to complete loop: ${err instanceof Error ? err.message : String(err)}`);
     }
 }
 export async function runLoopKill(loopRunId, opts) {
@@ -253,12 +897,12 @@ export async function runLoopKill(loopRunId, opts) {
         const res = await client.post(`/api/v1/loops/${loopRunId}/kill`);
         if (res.ok) {
             log.warn(`Loop run ${loopRunId} marked as KILLED.`);
-            const loopEnvPath = join(process.env.HOME || '', '.intutic', 'env', 'loop.env');
+            const loopEnvPath = join(getIntuticDir(), 'env', 'loop.env');
             await fs.rm(loopEnvPath, { force: true });
         }
     }
     catch (err) {
-        log.error(`Failed to kill loop: ${err.message}`);
+        log.error(`Failed to kill loop: ${err instanceof Error ? err.message : String(err)}`);
     }
 }
 export async function runLoopList(opts) {
@@ -270,13 +914,49 @@ export async function runLoopList(opts) {
             console.log(`  ${pc.bold('Loop Run ID')}           | ${pc.bold('Name')}           | ${pc.bold('Status')}    | ${pc.bold('Token Spend')} | ${pc.bold('Budget Limit')}`);
             console.log('  ' + '-'.repeat(85));
             for (const loop of res.loops) {
-                const statusStr = loop.status === 'ACTIVE' ? pc.green(loop.status) : loop.status === 'COMPLETED' ? pc.cyan(loop.status) : pc.red(loop.status);
+                // PENDING_REVIEW is amber, not red: it needs a person, but nothing has
+                // gone wrong. Falling through to the red branch made a held run look
+                // killed, which is the opposite of "waiting for you".
+                const statusStr = loop.status === 'ACTIVE'
+                    ? pc.green(loop.status)
+                    : loop.status === 'COMPLETED'
+                        ? pc.cyan(loop.status)
+                        : loop.status === 'PENDING_REVIEW'
+                            ? pc.yellow(loop.status)
+                            : pc.red(loop.status);
                 console.log(`  ${loop.loopRunId.padEnd(21)} | ${loop.name.padEnd(14)} | ${statusStr.padEnd(17)} | $${parseFloat(loop.totalTokenCostUsd).toFixed(4).padEnd(10)} | $${parseFloat(loop.budgetLimitUsd).toFixed(2)}`);
             }
         }
     }
     catch (err) {
-        log.error(`Failed to list loops: ${err.message}`);
+        log.error(`Failed to list loops: ${err instanceof Error ? err.message : String(err)}`);
+    }
+}
+/**
+ * Approve or reject a run held for human review.
+ *
+ * The other half of `review_before:`. Without it a hold has no resolution from
+ * the terminal, and the hold is deliberately permanent — there is no reaper, so
+ * an unreviewed run stays blocked until a person acts.
+ */
+export async function runLoopReview(loopRunId, opts) {
+    if (opts.approve === opts.reject) {
+        log.error('Specify exactly one of --approve or --reject.');
+        process.exit(1);
+    }
+    const action = opts.approve ? 'approve' : 'reject';
+    const client = await getClient(opts.dev);
+    try {
+        const res = await client.post(`/api/v1/loops/${loopRunId}/review`, { action, note: opts.note });
+        if (res.ok) {
+            log.success(action === 'approve'
+                ? `Loop run ${loopRunId} approved — it is ACTIVE again.`
+                : `Loop run ${loopRunId} rejected — it is KILLED.`);
+        }
+    }
+    catch (err) {
+        log.error(`Failed to resolve review: ${err instanceof Error ? err.message : String(err)}`);
+        process.exit(1);
     }
 }
 export async function runLoopExec(commandAndArgs, opts) {
@@ -325,25 +1005,50 @@ export async function runLoopExec(commandAndArgs, opts) {
             shell: true,
         });
         child.on('close', async (code) => {
+            // A non-zero exit is the agent failing, not governance stopping it. This used
+            // to POST /kill for that case, which conflated the two: KILLED means the
+            // circuit breaker or an operator intervened, and a run marked KILLED because
+            // the wrapped process returned 1 makes budget-breach data unreadable. It also
+            // meant the outcome was never recorded anywhere — the exit code was known
+            // right here and thrown away, leaving no way to tell a successful trajectory
+            // from a failed one afterwards.
+            // A held run is not finished, it is waiting. Completing it would close the
+            // review by side effect, with nothing recorded about who decided what — and
+            // the route refuses it anyway (400). The agent exits non-zero when the proxy
+            // returns 403, so without this check every hold ends in a confusing error.
+            try {
+                const current = await client.get(`/api/v1/loops/${loopRunId}`);
+                if (current?.loop?.status === 'PENDING_REVIEW') {
+                    log.warn('This loop run is held for human review — it has not finished.');
+                    log.info(`Approve or reject it:  intutic loop review ${loopRunId} --approve`);
+                    // loop.env is deliberately left in place: the resumed agent needs the
+                    // run id, and removing it here would orphan the run.
+                    process.exit(code || 0);
+                    return;
+                }
+            }
+            catch {
+                // Status unknown — fall through and record the outcome as usual rather
+                // than leaving the run open on a transient error.
+            }
             if (code === 0) {
-                await client.post(`/api/v1/loops/${loopRunId}/complete`).catch(() => { });
-                log.success(`Loop command execution succeeded. Wrapper loop marked COMPLETED.`);
+                await client
+                    .post(`/api/v1/loops/${loopRunId}/complete`, { outcome: 'SUCCEEDED' })
+                    .catch(() => { });
+                log.success('Loop command execution succeeded. Wrapper loop marked COMPLETED.');
             }
             else {
-                await client.post(`/api/v1/loops/${loopRunId}/kill`).catch(() => { });
-                log.warn(`Loop command execution exited with code ${code}. Wrapper loop marked KILLED.`);
+                await client
+                    .post(`/api/v1/loops/${loopRunId}/complete`, { outcome: 'FAILED' })
+                    .catch(() => { });
+                log.warn(`Loop command execution exited with code ${code}. Wrapper loop marked FAILED.`);
             }
             process.exit(code || 0);
         });
     }
     catch (err) {
-        log.error(`Loop execution wrapper failed: ${err.message}`);
+        log.error(`Loop execution wrapper failed: ${err instanceof Error ? err.message : String(err)}`);
         process.exit(1);
     }
 }
-function dirname(filePath) {
-    const parts = filePath.split('/');
-    parts.pop();
-    return parts.join('/');
-}
 //# sourceMappingURL=skill.js.map