@antomanc/aginit 0.4.0 → 0.5.0

package/dist/adapters/tool-ignores.js

@@ -0,0 +1,121 @@
+import path from 'node:path';
+import { fileExists, readTextFile, safeWriteFile } from '../utils/fs.js';
+import { readPackageManifest } from '../config/validation.js';
+// Vendored skill sources ship third-party JS and Markdown that the project's own
+// linters and formatters must not check. No ignore convention is shared across tools,
+// so each tool below says where its ignores live and how to add to them.
+const VENDORED_DIRS = ['.agents', '.claude'];
+const configs = (base, extensions) => extensions.map((ext) => `${base}${ext}`);
+/** Gitignore-syntax files: append the directories. */
+function ignoreFile(name, used) {
+    return {
+        file: (project) => (used(project) ? name : undefined),
+        missing: (text) => {
+            const lines = text.split(/\r?\n/).map((line) => line.trim().replace(/^\/|\/(\*\*)?$/g, ''));
+            return VENDORED_DIRS.filter((dir) => !lines.includes(dir));
+        },
+        patch: (text, dirs) => {
+            const block = `# Vendored agent skills (aginit)\n${dirs.map((dir) => `${dir}/`).join('\n')}\n`;
+            return text.trim() ? `${text.trimEnd()}\n\n${block}` : block;
+        },
+        advice: (file, dirs) => `add ${dirs.map((dir) => `${dir}/`).join(' and ')} to ${file}`
+    };
+}
+const prettier = ignoreFile('.prettierignore', (project) => project.has('prettier') ||
+    Boolean(project.manifest?.prettier) ||
+    [
+        ...configs('.prettierrc', ['', '.json', '.json5', '.yaml', '.yml', '.toml']),
+        ...configs('.prettierrc', ['.js', '.cjs', '.mjs', '.ts', '.cts', '.mts']),
+        ...configs('prettier.config', ['.js', '.cjs', '.mjs', '.ts', '.cts', '.mts'])
+    ].some(project.exists));
+// Legacy ESLint and oxlint read .eslintignore; flat-config ESLint does not.
+const eslintIgnore = ignoreFile('.eslintignore', (project) => project.has('oxlint') ||
+    Boolean(project.manifest?.eslintConfig) ||
+    configs('.eslintrc', ['', '.js', '.cjs', '.json', '.yaml', '.yml']).some(project.exists));
+/** Flat ESLint config: extend a global ignores array if there is an unambiguous one,
+ * `globalIgnores([...])` or an object holding only `ignores`. */
+const eslintFlat = {
+    file: (project) => configs('eslint.config', ['.js', '.mjs', '.cjs', '.ts', '.mts', '.cts']).find(project.exists),
+    missing: (text) => VENDORED_DIRS.filter((dir) => !text.includes(`${dir}/`)),
+    patch: (text, dirs) => {
+        const match = /globalIgnores\(\s*\[/.exec(text) ??
+            /\{\s*ignores\s*:\s*\[(?=[^[\]]*\]\s*,?\s*\})/.exec(text);
+        if (!match)
+            return null;
+        const at = match.index + match[0].length;
+        const rest = text.slice(at);
+        const quote = /^\s*(['"`])/.exec(rest)?.[1] ??
+            ((text.match(/"/g)?.length ?? 0) > (text.match(/'/g)?.length ?? 0) ? '"' : "'");
+        const entries = dirs.map((dir) => `${quote}${dir}/**${quote}`);
+        const indent = /^(\s*\n[ \t]*)/.exec(rest)?.[1];
+        const insertion = indent
+            ? entries.map((entry) => `${indent}${entry},`).join('')
+            : entries.join(', ') + (/^\s*\]/.test(rest) ? '' : ', ');
+        return text.slice(0, at) + insertion + rest;
+    },
+    advice: (file, dirs) => `add { ignores: [${dirs.map((dir) => `'${dir}/**'`).join(', ')}] } to the exported array in ${file}`
+};
+/** Biome 2.2+: force-ignore the folders through files.includes. */
+const biome = {
+    file: (project) => ['biome.json', 'biome.jsonc'].find(project.exists),
+    missing: (text) => VENDORED_DIRS.filter((dir) => !text.includes(`**/${dir}`)),
+    patch: (text, dirs) => {
+        let config;
+        try {
+            config = JSON.parse(text); // a biome.jsonc with comments gets advice instead
+        }
+        catch {
+            return null;
+        }
+        const includes = config.files?.includes ?? ['**'];
+        if (!Array.isArray(includes))
+            return null;
+        config.files = {
+            ...config.files,
+            includes: [...includes, ...dirs.map((dir) => `!!**/${dir}`)]
+        };
+        const json = JSON.stringify(config, null, /\n([ \t]+)"/.exec(text)?.[1] ?? 2) + '\n';
+        // Like Biome's formatter, keep the array on one line when it fits in 80 columns.
+        return json.replace(/^([ \t]*"includes": )\[[^\]]*\]/m, (block, key) => {
+            const inline = `${key}[${config.files.includes.map((p) => JSON.stringify(p)).join(', ')}]`;
+            return inline.replace(/\t/g, '  ').length <= 80 ? inline : block;
+        });
+    },
+    advice: (file, dirs) => `add ${dirs.map((dir) => `"!!**/${dir}"`).join(', ')} to files.includes in ${file}`
+};
+const TOOLS = [prettier, eslintIgnore, eslintFlat, biome];
+function pendingIgnores(targetDir) {
+    const manifest = readPackageManifest(targetDir);
+    const project = {
+        manifest,
+        has: (name) => Boolean(manifest?.dependencies?.[name] || manifest?.devDependencies?.[name]),
+        exists: (file) => fileExists(path.join(targetDir, file))
+    };
+    return TOOLS.flatMap((tool) => {
+        const file = tool.file(project);
+        if (!file)
+            return [];
+        const text = readTextFile(path.join(targetDir, file)) ?? '';
+        const missing = tool.missing(text);
+        return missing.length > 0 ? [{ tool, file, text, missing }] : [];
+    });
+}
+/** Keeps the project's linters and formatters off vendored skills. Returns the
+ * advice for configs that could not be edited safely. */
+export function ignoreVendoredSkills(targetDir, options = {}) {
+    const { dryRun = false, silent = false } = options;
+    const advice = [];
+    for (const { tool, file, text, missing } of pendingIgnores(targetDir)) {
+        const patched = tool.patch(text, missing);
+        if (patched === null)
+            advice.push(`Linters check vendored skills: ${tool.advice(file, missing)}`);
+        else
+            safeWriteFile(path.join(targetDir, file), patched, { overwrite: true, dryRun, silent });
+    }
+    return advice;
+}
+/** Doctor view: every config that still lets a linter or formatter see vendored skills. */
+export function vendoredSkillsExposure(targetDir) {
+    return pendingIgnores(targetDir).map(({ tool, file, missing }) => tool.advice(file, missing));
+}
+//# sourceMappingURL=tool-ignores.js.map

package/dist/adapters/tool-ignores.js.map

@@ -0,0 +1 @@
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package/dist/cli/capabilities.d.ts

@@ -0,0 +1,17 @@
+/** Print the registry grouped by category, marking what the project has enabled. */
+export declare function listCapabilities(targetDir?: string): void;
+export interface ChangeOptions {
+    dryRun?: boolean;
+    silent?: boolean;
+}
+/**
+ * Enable or disable capabilities, then bring the project in line: config,
+ * skills (installed or removed through the Skills CLI), upstream setups,
+ * AGENTS.md and docs/agents/. Picking a methodology, design or UI driver
+ * replaces the current one in that category.
+ */
+export declare function changeCapabilities(targetDir: string, change: {
+    add?: string[];
+    remove?: string[];
+}, options?: ChangeOptions): Promise<boolean>;
+//# sourceMappingURL=capabilities.d.ts.map

package/dist/cli/capabilities.d.ts.map

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package/dist/cli/capabilities.js

@@ -0,0 +1,149 @@
+import path from 'node:path';
+import pc from 'picocolors';
+import { AGINIT_CONFIG_FILENAME } from '../config/schema.js';
+import { readProjectConfig, validateConfig } from '../config/validation.js';
+import { resolvePlatformStack } from '../adapters/agent-docs.js';
+import { installAllSkills, removeSkills, skillAgents } from '../adapters/skills.js';
+import { uninstallGraft } from '../adapters/graft.js';
+import { ignoreVendoredSkills } from '../adapters/tool-ignores.js';
+import { activeIds, applyResolvedProfile, catalogFor, findCapability, inferCapabilities, resolveCapabilities, sourcesFor } from '../registry/index.js';
+import { SETUPS } from '../registry/setup.js';
+import { writeJsonFile } from '../utils/fs.js';
+import { logger } from '../utils/logger.js';
+import { missingBinaries, syncAgentDocs } from './new.js';
+const CATEGORY_ORDER = [
+    'codebase-graph',
+    'methodology',
+    'discipline',
+    'design',
+    'ui-driver',
+    'testing-engine',
+    'context-guard',
+    'custom'
+];
+/** Print the registry grouped by category, marking what the project has enabled. */
+export function listCapabilities(targetDir = process.cwd()) {
+    const config = readProjectConfig(targetDir);
+    const enabled = config ? activeIds(config) : new Set();
+    logger.banner('Aginit — Capability registry', config ? `Enabled in ${AGINIT_CONFIG_FILENAME}: ●` : `No ${AGINIT_CONFIG_FILENAME} here; showing the catalog`);
+    const catalog = catalogFor(config);
+    for (const category of CATEGORY_ORDER) {
+        const entries = catalog.filter((c) => c.category === category);
+        if (entries.length === 0)
+            continue;
+        console.log(pc.bold(pc.underline(category)));
+        for (const c of entries) {
+            const mark = enabled.has(c.id) ? pc.green('●') : pc.dim('○');
+            const platforms = c.supportedPlatforms.join(', ');
+            console.log(`  ${mark} ${pc.bold(c.id.padEnd(22))} ${c.description}`);
+            console.log(pc.dim(`      ${platforms} · ${c.license} · ${c.repoUrl}`));
+        }
+        console.log();
+    }
+}
+function requireConfig(targetDir) {
+    const config = readProjectConfig(targetDir);
+    if (!config)
+        throw new Error(`No ${AGINIT_CONFIG_FILENAME} in ${targetDir}. Run \`aginit init\` first.`);
+    return config;
+}
+/** Skill names to remove; a source installed whole is removed by its repo. */
+const skillsOf = (capabilities) => capabilities.flatMap((c) => c.install.flatMap((s) => (s.kind !== 'skills-sh' ? [] : s.skills.length ? s.skills : [s.repo])));
+/**
+ * Enable or disable capabilities, then bring the project in line: config,
+ * skills (installed or removed through the Skills CLI), upstream setups,
+ * AGENTS.md and docs/agents/. Picking a methodology, design or UI driver
+ * replaces the current one in that category.
+ */
+export async function changeCapabilities(targetDir, change, options = {}) {
+    const { dryRun = false, silent = false } = options;
+    const config = requireConfig(targetDir);
+    const { platform, stack } = resolvePlatformStack(config, targetDir);
+    const base = config.capabilities ?? inferCapabilities(config);
+    const previous = [...base, ...(config.customCapabilities ?? []).map((c) => c.id)];
+    const before = activeIds(config);
+    const flags = { addons: [], addSkills: [], without: [] };
+    for (const id of change.add ?? []) {
+        const capability = findCapability(id, config);
+        if (!capability) {
+            if (id.includes('/'))
+                flags.addSkills.push(id);
+            else
+                throw new Error(`Unknown capability "${id}". Run \`aginit list\` to see the registry.`);
+        }
+        else if (capability.category === 'methodology')
+            flags.methodology = id;
+        else if (capability.category === 'design')
+            flags.design = id;
+        else if (capability.category === 'ui-driver' && !capability.addon)
+            flags.uiDriver = id;
+        else
+            flags.addons.push(id);
+    }
+    for (const id of change.remove ?? []) {
+        if (!findCapability(id, config))
+            throw new Error(`Unknown capability "${id}". Run \`aginit list\` to see the registry.`);
+        flags.without.push(id);
+    }
+    const custom = config.customCapabilities ?? [];
+    const customIds = new Set(custom.map((c) => c.id));
+    const disabled = (config.disabledCapabilities ?? []).filter((id) => !(change.add ?? []).includes(id));
+    const resolved = resolveCapabilities({ platform, stack, framework: config.framework, base, basePlatform: platform, flags, custom }, disabled);
+    // A removed custom capability is gone, not disabled.
+    resolved.disabledCapabilities = resolved.disabledCapabilities.filter((id) => !customIds.has(id));
+    const next = validateConfig(applyResolvedProfile({ ...config, platform, stack }, resolved, { skills: true, previous }));
+    // Adding graft or playwright turns their legacy switch back on.
+    if (next.capabilities?.includes('graft'))
+        next.codebase.graft = true;
+    const after = activeIds(next);
+    const nextCatalog = catalogFor(next);
+    const added = nextCatalog.filter((c) => after.has(c.id) && !before.has(c.id));
+    const removed = catalogFor(config).filter((c) => before.has(c.id) && !after.has(c.id));
+    if (added.length === 0 && removed.length === 0 && JSON.stringify(next) === JSON.stringify(config)) {
+        if (!silent)
+            logger.info('Nothing to change.');
+        return true;
+    }
+    if (!silent) {
+        for (const c of added)
+            logger.success(`Enabling ${c.id}`);
+        for (const c of removed)
+            logger.warn(`Disabling ${c.id}`);
+    }
+    writeJsonFile(path.join(targetDir, AGINIT_CONFIG_FILENAME), next, { overwrite: true, dryRun, silent });
+    let ok = true;
+    ok = (await removeSkills(targetDir, skillsOf(removed), { dryRun, silent })) && ok;
+    if (removed.some((c) => c.id === 'graft'))
+        await uninstallGraft(targetDir, { dryRun, silent });
+    const leftovers = removed.filter((c) => c.install.some((s) => s.kind === 'setup' && s.setup !== 'graft'));
+    if (!silent)
+        for (const c of leftovers)
+            logger.dim(`${c.id}: files and global CLIs its setup created are left in place; remove them by hand.`);
+    const addedSources = sourcesFor(added);
+    if (addedSources.length > 0) {
+        const { failed } = await installAllSkills(targetDir, addedSources, {
+            agents: skillAgents(next),
+            dryRun,
+            silent
+        });
+        ok = failed.length === 0 && ok;
+        for (const line of ignoreVendoredSkills(targetDir, { dryRun, silent: true }))
+            logger.warn(line);
+    }
+    for (const c of added)
+        for (const step of c.install)
+            if (step.kind === 'setup')
+                ok = (await SETUPS[step.setup]({ targetDir, config: next, platform, stack, dryRun, silent })) && ok;
+    syncAgentDocs(targetDir, next, { dryRun, silent });
+    if (!silent)
+        for (const { name, bin, install } of await missingBinaries(added, ['graft', 'agent-browser', 'e2e']))
+            logger.warn(`${name} needs the \`${bin}\` CLI: ${install}`);
+    if (!silent) {
+        if (ok)
+            logger.success('Capabilities updated. AGENTS.md and docs/agents/ are in sync.');
+        else
+            logger.warn('Capabilities updated with warnings. Resolve them and rerun `aginit init`.');
+    }
+    return ok;
+}
+//# sourceMappingURL=capabilities.js.map

package/dist/cli/capabilities.js.map

@@ -0,0 +1 @@
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package/dist/cli/doctor.d.ts

@@ -1,2 +1,18 @@
+import { AginitConfig } from '../config/schema.js';
+/**
+ * One row per active capability, built from its registry entry: every skill
+ * file it installs, every CLI it drives and any artifact it declares.
+ */
+export declare function capabilityChecks(targetDir: string, config: AginitConfig): Promise<CheckItem[]>;
+type CheckCategory = 'Environment' | 'AI Tooling' | 'Project Config' | 'Capabilities';
+interface CheckItem {
+    name: string;
+    category: CheckCategory;
+    ok: boolean;
+    version?: string;
+    detail: string;
+    suggestion?: string;
+}
 export declare function runDoctor(targetDir?: string): Promise<void>;
+export {};
 //# sourceMappingURL=doctor.d.ts.map

package/dist/cli/doctor.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"doctor.d.ts","sourceRoot":"","sources":["../../src/cli/doctor.ts"],"names":[],"mappings":"AAoCA,wBAAsB,SAAS,CAAC,SAAS,GAAE,MAAsB,GAAG,OAAO,CAAC,IAAI,CAAC,CA+UhF"}
+{"version":3,"file":"doctor.d.ts","sourceRoot":"","sources":["../../src/cli/doctor.ts"],"names":[],"mappings":"AAIA,OAAO,EAGL,YAAY,EAEb,MAAM,qBAAqB,CAAC;AAoB7B;;;GAGG;AACH,wBAAsB,gBAAgB,CACpC,SAAS,EAAE,MAAM,EACjB,MAAM,EAAE,YAAY,GACnB,OAAO,CAAC,SAAS,EAAE,CAAC,CAqCtB;AAED,KAAK,aAAa,GAAG,aAAa,GAAG,YAAY,GAAG,gBAAgB,GAAG,cAAc,CAAC;AAEtF,UAAU,SAAS;IACjB,IAAI,EAAE,MAAM,CAAC;IACb,QAAQ,EAAE,aAAa,CAAC;IACxB,EAAE,EAAE,OAAO,CAAC;IACZ,OAAO,CAAC,EAAE,MAAM,CAAC;IACjB,MAAM,EAAE,MAAM,CAAC;IACf,UAAU,CAAC,EAAE,MAAM,CAAC;CACrB;AAED,wBAAsB,SAAS,CAAC,SAAS,GAAE,MAAsB,GAAG,OAAO,CAAC,IAAI,CAAC,CA+ThF"}

package/dist/cli/doctor.js

@@ -7,9 +7,58 @@ import { detectPackageManager } from '../adapters/package-manager.js';
 import fs from 'node:fs';
 import { claudeCodeEnabled, getInstalledSkills, getSkillsMissingForClaude } from '../adapters/skills.js';
 import { claudeMarkdownImportsAgents } from '../adapters/agents-md.js';
-import { agentBrowserConfigured, agentBrowserStubInstalled, findUsernsRestriction, runAgentBrowserDiagnostics } from '../adapters/agent-browser.js';
+import { agentBrowserStubInstalled, findUsernsRestriction, runAgentBrowserDiagnostics } from '../adapters/agent-browser.js';
 import { readProjectConfig } from '../config/validation.js';
+import { vendoredSkillsExposure } from '../adapters/tool-ignores.js';
 import { logger } from '../utils/logger.js';
+import { activeCapabilities, activeIds, doctorChecks, isNodeStack } from '../registry/index.js';
+import { resolvePlatformStack } from '../adapters/agent-docs.js';
+/**
+ * One row per active capability, built from its registry entry: every skill
+ * file it installs, every CLI it drives and any artifact it declares.
+ */
+export async function capabilityChecks(targetDir, config) {
+    const items = [];
+    for (const capability of activeCapabilities(config)) {
+        const problems = [];
+        const fixes = [];
+        const missingSkills = [];
+        const versions = [];
+        for (const check of doctorChecks(capability, config.skills.sources)) {
+            if (check.kind === 'file') {
+                if (fileExists(path.join(targetDir, check.path)))
+                    continue;
+                const skill = /^\.agents\/skills\/([^/]+)\/SKILL\.md$/.exec(check.path)?.[1];
+                if (skill)
+                    missingSkills.push(skill);
+                else {
+                    problems.push(`${check.path} missing`);
+                    fixes.push(check.fix);
+                }
+            }
+            else if (!(await commandExists(check.bin))) {
+                problems.push(`${check.bin} CLI not found in PATH`);
+                fixes.push(check.fix);
+            }
+            else {
+                const res = await runExecutable(check.bin, check.args, { silent: true, timeout: 30_000 });
+                versions.push(res.ok && res.stdout ? `${check.bin} ${res.stdout.split('\n')[0]}` : check.bin);
+            }
+        }
+        if (missingSkills.length) {
+            problems.unshift(`skills missing from .agents/skills/: ${missingSkills.join(', ')}`);
+            fixes.unshift('Run `aginit init` to reinstall the configured skills');
+        }
+        items.push({
+            name: `${capability.name} (${capability.category})`,
+            category: 'Capabilities',
+            ok: problems.length === 0,
+            detail: problems.length ? problems.join('; ') : `Ready${versions.length ? ` (${versions.join(', ')})` : ''}`,
+            suggestion: fixes.length ? fixes.join(' · ') : undefined
+        });
+    }
+    return items;
+}
 export async function runDoctor(targetDir = process.cwd()) {
     logger.banner('Aginit — System & Project Doctor', `Target: ${targetDir}`);
     // Resolve project config early to detect configured package manager
@@ -58,18 +107,24 @@ export async function runDoctor(targetDir = process.cwd()) {
         detail: nodeDetail,
         suggestion: nodeSuggestion
     });
-    // 2. Active Package Manager check (pnpm, npm, yarn, or bun)
-    const pmRes = await runExecutable(activePm, ['-v'], { silent: true });
-    checks.push({
-        name: `${activePm} package manager`,
-        category: 'Environment',
-        ok: pmRes.ok,
-        version: pmRes.stdout,
-        detail: pmRes.ok ? `Installed (${pmRes.stdout})` : `${activePm} is not found in PATH`,
-        suggestion: pmRes.ok
-            ? undefined
-            : `Install ${activePm} (${activePm === 'pnpm' ? 'npm install -g pnpm' : activePm === 'bun' ? 'curl -fsSL https://bun.sh/install | bash' : 'install ' + activePm})`
-    });
+    // 2. Active Package Manager check (pnpm, npm, yarn, or bun); none for non-Node stacks
+    const { stack, platform } = projectConfig
+        ? resolvePlatformStack(projectConfig, targetDir)
+        : { stack: 'node', platform: null };
+    const pmRes = isNodeStack(stack)
+        ? await runExecutable(activePm, ['-v'], { silent: true })
+        : null;
+    if (pmRes)
+        checks.push({
+            name: `${activePm} package manager`,
+            category: 'Environment',
+            ok: pmRes.ok,
+            version: pmRes.stdout,
+            detail: pmRes.ok ? `Installed (${pmRes.stdout})` : `${activePm} is not found in PATH`,
+            suggestion: pmRes.ok
+                ? undefined
+                : `Install ${activePm} (${activePm === 'pnpm' ? 'npm install -g pnpm' : activePm === 'bun' ? 'curl -fsSL https://bun.sh/install | bash' : 'install ' + activePm})`
+        });
     // 3. Git check
     const gitExists = await commandExists('git');
     let isGitRepo = fileExists(path.join(targetDir, '.git'));
@@ -101,21 +156,6 @@ export async function runDoctor(targetDir = process.cwd()) {
                 ? 'Run `git init` or `aginit init` to initialize repository'
                 : undefined
     });
-    // 4. Graft CLI check
-    const graftExists = await commandExists('graft');
-    let graftVersion = '';
-    if (graftExists) {
-        const gv = await runExecutable('graft', ['--version'], { silent: true });
-        graftVersion = gv.stdout;
-    }
-    checks.push({
-        name: 'Graft codebase graph CLI',
-        category: 'AI Tooling',
-        ok: graftExists,
-        version: graftVersion,
-        detail: graftExists ? `Installed globally (${graftVersion})` : 'Graft CLI not found in PATH',
-        suggestion: graftExists ? undefined : 'Install Graft: `npm install -g @nanonets/graft`'
-    });
     // 5. Codex CLI check
     const codexExists = await commandExists('codex');
     checks.push({
@@ -141,7 +181,7 @@ export async function runDoctor(targetDir = process.cwd()) {
         category: 'Project Config',
         ok: !!projectConfig,
         detail: projectConfig
-            ? `Preset: "${projectConfig.preset}" (v${projectConfig.schemaVersion || '1.0.0'}), pm: ${activePm}, agents: ${projectConfig.agents.primary}/${projectConfig.agents.secondary}${claudeCodeEnabled(projectConfig) ? '/claude-code' : ''}`
+            ? `Preset: "${projectConfig.preset}" (v${projectConfig.schemaVersion || '1.0.0'}), platform: ${platform} (${stack})${pmRes ? `, pm: ${activePm}` : ''}, agents: ${projectConfig.agents.primary}/${projectConfig.agents.secondary}${claudeCodeEnabled(projectConfig) ? '/claude-code' : ''}`
             : configError
                 ? `Invalid configuration: ${configError}`
                 : 'No aginit.config.json found in current directory',
@@ -187,6 +227,19 @@ export async function runDoctor(targetDir = process.cwd()) {
             ? undefined
             : 'Run `aginit init` or `npx skills add ...` to install skills'
     });
+    // 9a. Vendored skills must stay out of the project's linters and formatters
+    if (installedSkills.length > 0) {
+        const exposure = vendoredSkillsExposure(targetDir);
+        checks.push({
+            name: 'Lint/format ignores for vendored skills',
+            category: 'Project Config',
+            ok: exposure.length === 0,
+            detail: exposure.length === 0
+                ? 'Detected linters and formatters skip .agents/ and .claude/'
+                : 'Project linters or formatters will check vendored skill files',
+            suggestion: exposure.length === 0 ? undefined : `Run \`aginit update\`, or ${exposure.join('; ')}`
+        });
+    }
     // 9b. Claude Code: skills linked into .claude/skills/ and AGENTS.md reachable
     if (projectConfig !== null && claudeCodeEnabled(projectConfig)) {
         if (!skillsDisabled && installedSkills.length > 0) {
@@ -228,43 +281,26 @@ export async function runDoctor(targetDir = process.cwd()) {
                     : 'Add a line `@AGENTS.md` to CLAUDE.md'
         });
     }
+    // 10. Registry: each active capability's checks (skill files, CLIs, artifacts)
+    if (projectConfig !== null)
+        checks.push(...(await capabilityChecks(targetDir, projectConfig)));
     // 10. agent-browser runtime (only when the project ships the skill)
     const agentBrowserWanted = projectConfig !== null &&
-        (agentBrowserConfigured(projectConfig.skills.sources) || agentBrowserStubInstalled(targetDir));
-    if (agentBrowserWanted) {
-        const abExists = await commandExists('agent-browser');
-        let abVersion = '';
-        if (abExists) {
-            const av = await runExecutable('agent-browser', ['--version'], { silent: true });
-            abVersion = av.ok ? av.stdout : '';
-        }
-        checks.push({
-            name: 'agent-browser CLI',
-            category: 'AI Tooling',
-            ok: abExists,
-            version: abVersion,
-            detail: abExists
-                ? `Installed globally (${abVersion || 'version unknown'})`
-                : 'agent-browser skill is installed but the CLI is not in PATH',
-            suggestion: abExists
-                ? undefined
-                : 'Install the runtime: `npm i -g agent-browser && agent-browser install`'
-        });
-        if (abExists) {
-            const diagnostics = await runAgentBrowserDiagnostics();
-            if (diagnostics !== null) {
-                checks.push({
-                    name: 'agent-browser browser runtime',
-                    category: 'AI Tooling',
-                    ok: diagnostics.length === 0,
-                    detail: diagnostics.length === 0
-                        ? 'Upstream doctor reports browser and launch environment healthy'
-                        : diagnostics.map((d) => d.message).join('; '),
-                    suggestion: diagnostics.length === 0
-                        ? undefined
-                        : (diagnostics.find((d) => d.fix)?.fix ?? 'Run `agent-browser doctor` for details')
-                });
-            }
+        (activeIds(projectConfig).has('agent-browser') || agentBrowserStubInstalled(targetDir));
+    if (agentBrowserWanted && (await commandExists('agent-browser'))) {
+        const diagnostics = await runAgentBrowserDiagnostics();
+        if (diagnostics !== null) {
+            checks.push({
+                name: 'agent-browser browser runtime',
+                category: 'AI Tooling',
+                ok: diagnostics.length === 0,
+                detail: diagnostics.length === 0
+                    ? 'Upstream doctor reports browser and launch environment healthy'
+                    : diagnostics.map((d) => d.message).join('; '),
+                suggestion: diagnostics.length === 0
+                    ? undefined
+                    : (diagnostics.find((d) => d.fix)?.fix ?? 'Run `agent-browser doctor` for details')
+            });
         }
     }
     // 11. Chrome sandbox prerequisites — agent-browser and Playwright both
@@ -291,14 +327,12 @@ export async function runDoctor(targetDir = process.cwd()) {
         }
     }
     // Print grouped results
-    const categories = [
-        'Environment',
-        'AI Tooling',
-        'Project Config'
-    ];
+    const categories = ['Environment', 'AI Tooling', 'Project Config', 'Capabilities'];
     for (const cat of categories) {
-        console.log(pc.bold(pc.underline(cat)));
         const catChecks = checks.filter((c) => c.category === cat);
+        if (catChecks.length === 0)
+            continue;
+        console.log(pc.bold(pc.underline(cat)));
         for (const c of catChecks) {
             const icon = c.ok ? pc.green('✓') : pc.yellow('⚠');
             const name = pc.bold(c.name);