refactor: reorganize src/ from flat files into deep modules

scripts/sync-agents.ts

@@ -3,7 +3,7 @@
 import { readFileSync, writeFileSync } from 'fs';
 import { join } from 'path';
 import { homedir } from 'os';
-import { agents } from '../src/agents.ts';
+import { agents } from '../src/lib/agents/agents.ts';
 
 const ROOT = join(import.meta.dirname, '..');
 const README_PATH = join(ROOT, 'README.md');

scripts/validate-agents.ts

@@ -1,6 +1,6 @@
 #!/usr/bin/env node
 
-import { agents } from '../src/agents.ts';
+import { agents } from '../src/lib/agents/agents.ts';
 
 let hasErrors = false;
 

src/add-agents.test.ts → src/add/add-agents.test.ts

@@ -1,13 +1,13 @@
 import { describe, it, expect, vi, beforeEach } from 'vitest';
-import { multiselect, promptForAgents, selectAgentsInteractive } from './add-agents.js';
-import * as skillLock from './skill-lock.js';
-import * as searchMultiselectModule from './prompts/search-multiselect.js';
+import { multiselect, promptForAgents, selectAgentsInteractive } from './add-agents.ts';
+import * as skillLock from '../lib/lock/skill-lock.ts';
+import * as searchMultiselectModule from '../lib/prompts/search-multiselect.ts';
 import * as clack from '@clack/prompts';
-import * as agentsModule from './agents.js';
+import * as agentsModule from '../lib/agents/agents.ts';
 
 // Mock dependencies
-vi.mock('./skill-lock.js');
-vi.mock('./prompts/search-multiselect.js');
+vi.mock('../lib/lock/skill-lock.ts');
+vi.mock('../lib/prompts/search-multiselect.ts');
 vi.mock('@clack/prompts', async () => {
   const actual = await vi.importActual('@clack/prompts');
   return {

src/add-agents.ts → src/add/add-agents.ts

@@ -1,9 +1,9 @@
 import * as p from '@clack/prompts';
 import pc from 'picocolors';
-import { searchMultiselect } from './prompts/search-multiselect.ts';
-import { agents, getUniversalAgents, getNonUniversalAgents } from './agents.ts';
-import { getLastSelectedAgents, saveSelectedAgents } from './skill-lock.ts';
-import type { AgentType } from './types.ts';
+import { searchMultiselect } from '../lib/prompts/search-multiselect.ts';
+import { agents, getUniversalAgents, getNonUniversalAgents } from '../lib/agents/index.ts';
+import { getLastSelectedAgents, saveSelectedAgents } from '../lib/lock/index.ts';
+import type { AgentType } from '../lib/types.ts';
 
 // Helper to check if a value is a cancel symbol (works with both clack and our custom prompts)
 const isCancelled = (value: unknown): value is symbol => typeof value === 'symbol';

src/add-display.test.ts → src/add/add-display.test.ts

@@ -9,8 +9,8 @@ import {
   ensureUniversalAgents,
   buildResultLines,
 } from './add-display.ts';
-import type { AgentType } from './types.ts';
-import type { AuditResponse, PartnerAudit } from './telemetry.ts';
+import type { AgentType } from '../lib/types.ts';
+import type { AuditResponse, PartnerAudit } from '../lib/telemetry.ts';
 
 // Helper to strip ANSI escape codes for easier assertion
 const stripAnsi = (s: string) => s.replace(/\x1b\[[0-9;]*m/g, '');

src/add-display.ts → src/add/add-display.ts

@@ -1,9 +1,9 @@
 import pc from 'picocolors';
-import { formatList } from './utils.ts';
-import { agents, getUniversalAgents, isUniversalAgent } from './agents.ts';
-import type { AgentType } from './types.ts';
-import type { InstallMode } from './skill-installer.ts';
-import type { AuditResponse, PartnerAudit } from './telemetry.ts';
+import { formatList } from '../lib/utils.ts';
+import { agents, getUniversalAgents, isUniversalAgent } from '../lib/agents/index.ts';
+import type { AgentType } from '../lib/types.ts';
+import type { InstallMode } from '../lib/install/index.ts';
+import type { AuditResponse, PartnerAudit } from '../lib/telemetry.ts';
 
 // ─── Security Advisory ───
 

src/add-install.test.ts → src/add/add-install.test.ts

@@ -1,6 +1,6 @@
 import { describe, it, expect, vi, beforeEach, afterEach } from 'vitest';
 import type { AddOptions } from './add-options.ts';
-import type { AgentType } from './types.ts';
+import type { AgentType } from '../lib/types.ts';
 
 // --- Mocks ---
 
@@ -18,8 +18,8 @@ vi.mock('@clack/prompts', async () => {
   };
 });
 
-vi.mock('./agents.ts', async () => {
-  const actual = await vi.importActual('./agents.ts');
+vi.mock('../lib/agents/agents.ts', async () => {
+  const actual = await vi.importActual('../lib/agents/agents.ts');
   return {
     ...actual,
     detectInstalledAgents: vi.fn(),
@@ -32,8 +32,8 @@ vi.mock('./add-agents.ts', () => ({
   selectAgentsInteractive: vi.fn(),
 }));
 
-vi.mock('./skill-installer.ts', async () => {
-  const actual = await vi.importActual('./skill-installer.ts');
+vi.mock('../lib/install/skill-installer.ts', async () => {
+  const actual = await vi.importActual('../lib/install/skill-installer.ts');
   return {
     ...actual,
     isSkillInstalled: vi.fn(),
@@ -49,10 +49,10 @@ import {
   displayInstallResults,
   type InstallResult,
 } from './add-install.ts';
-import { detectInstalledAgents, agents } from './agents.ts';
+import { detectInstalledAgents, agents } from '../lib/agents/index.ts';
 import { promptForAgents, selectAgentsInteractive } from './add-agents.ts';
-import { isSkillInstalled } from './skill-installer.ts';
-import { CommandError } from './command-result.ts';
+import { isSkillInstalled } from '../lib/install/index.ts';
+import { CommandError } from '../lib/command-result.ts';
 
 // --- Helpers ---
 

src/add-install.ts → src/add/add-install.ts

@@ -1,13 +1,13 @@
 import * as p from '@clack/prompts';
 import pc from 'picocolors';
 import { promptForAgents, selectAgentsInteractive } from './add-agents.ts';
-import { isSkillInstalled, type InstallMode } from './skill-installer.ts';
-import { detectInstalledAgents, agents } from './agents.ts';
-import type { AgentType } from './types.ts';
+import { isSkillInstalled, type InstallMode } from '../lib/install/index.ts';
+import { detectInstalledAgents, agents } from '../lib/agents/index.ts';
+import type { AgentType } from '../lib/types.ts';
 import { ensureUniversalAgents, buildResultLines } from './add-display.ts';
 import type { AddOptions } from './add-options.ts';
-import { shortenPath, formatList, kebabToTitle } from './utils.ts';
-import { CommandError } from './command-result.ts';
+import { shortenPath, formatList, kebabToTitle } from '../lib/utils.ts';
+import { CommandError } from '../lib/command-result.ts';
 
 export interface InstallResult {
   skill: string;

src/add-options.test.ts → src/add/add-options.test.ts

@@ -1,6 +1,6 @@
 import { describe, it, expect } from 'vitest';
 import { parseAddOptions } from './add-options.ts';
-import { resolveTargetAgents } from './context-add.ts';
+import { resolveTargetAgents } from '../lib/install/index.ts';
 
 // ---------------------------------------------------------------------------
 // parseAddOptions — basic flags

src/add-options.ts → src/add/add-options.ts

@@ -1,5 +1,5 @@
-import type { ContextType } from './types.ts';
-import { consumeMultiValues } from './cli-parse.ts';
+import type { ContextType } from '../lib/types.ts';
+import { consumeMultiValues } from '../cli-parse.ts';
 
 export interface AddOptions {
   global?: boolean;

src/add-prompt.test.ts → src/add/add-prompt.test.ts

@@ -1,16 +1,16 @@
 import { describe, it, expect, vi, beforeEach } from 'vitest';
-import { promptForAgents } from './add.js';
-import * as skillLock from './skill-lock.js';
-import * as searchMultiselectModule from './prompts/search-multiselect.js';
+import { promptForAgents } from './add.ts';
+import * as skillLock from '../lib/lock/skill-lock.ts';
+import * as searchMultiselectModule from '../lib/prompts/search-multiselect.ts';
 
 // Mock dependencies
-vi.mock('./skill-lock.js');
-vi.mock('./prompts/search-multiselect.js');
-vi.mock('./telemetry.js', () => ({
+vi.mock('../lib/lock/skill-lock.ts');
+vi.mock('../lib/prompts/search-multiselect.ts');
+vi.mock('../lib/telemetry.ts', () => ({
   setVersion: vi.fn(),
   track: vi.fn(),
 }));
-vi.mock('../package.json', () => ({
+vi.mock('../../package.json', () => ({
   default: { version: '1.0.0' },
 }));
 

src/add-wellknown.test.ts → src/add/add-wellknown.test.ts

@@ -1,7 +1,7 @@
 import { describe, it, expect, vi, beforeEach, afterEach } from 'vitest';
-import type { WellKnownSkill } from './providers/index.ts';
+import type { WellKnownSkill } from '../lib/providers/index.ts';
 import type { AddOptions } from './add-options.ts';
-import type { AgentType } from './types.ts';
+import type { AgentType } from '../lib/types.ts';
 
 // --- Mocks ---
 
@@ -18,23 +18,23 @@ vi.mock('@clack/prompts', async () => {
   };
 });
 
-vi.mock('./providers/index.ts', () => ({
+vi.mock('../lib/providers/index.ts', () => ({
   wellKnownProvider: {
     fetchAllSkills: vi.fn(),
     getSourceIdentifier: vi.fn().mockReturnValue('wellknown/example.com'),
   },
 }));
 
-vi.mock('./agents.ts', async () => {
-  const actual = await vi.importActual('./agents.ts');
+vi.mock('../lib/agents/agents.ts', async () => {
+  const actual = await vi.importActual('../lib/agents/agents.ts');
   return {
     ...actual,
     detectInstalledAgents: vi.fn(),
   };
 });
 
-vi.mock('./skill-installer.ts', async () => {
-  const actual = await vi.importActual('./skill-installer.ts');
+vi.mock('../lib/install/skill-installer.ts', async () => {
+  const actual = await vi.importActual('../lib/install/skill-installer.ts');
   return {
     ...actual,
     isSkillInstalled: vi.fn().mockResolvedValue(false),
@@ -49,21 +49,21 @@ vi.mock('./add-agents.ts', () => ({
   selectAgentsInteractive: vi.fn(),
 }));
 
-vi.mock('./telemetry.ts', () => ({
+vi.mock('../lib/telemetry.ts', () => ({
   track: vi.fn(),
 }));
 
-vi.mock('./skill-lock.ts', () => ({
+vi.mock('../lib/lock/skill-lock.ts', () => ({
   addSkillToLock: vi.fn(),
 }));
 
-vi.mock('./local-lock.ts', () => ({
+vi.mock('../lib/lock/local-lock.ts', () => ({
   addSkillToLocalLock: vi.fn(),
   computeSkillFolderHash: vi.fn().mockResolvedValue('abc123'),
 }));
 
-vi.mock('./source-parser.ts', async () => {
-  const actual = await vi.importActual('./source-parser.ts');
+vi.mock('../lib/parsers/source-parser.ts', async () => {
+  const actual = await vi.importActual('../lib/parsers/source-parser.ts');
   return {
     ...actual,
     isSourcePrivate: vi.fn().mockResolvedValue(false),
@@ -74,14 +74,14 @@ vi.mock('./source-parser.ts', async () => {
 
 import * as p from '@clack/prompts';
 import { handleWellKnownSkills } from './add-wellknown.ts';
-import { wellKnownProvider } from './providers/index.ts';
-import { detectInstalledAgents } from './agents.ts';
-import { isSkillInstalled, installWellKnownSkillForAgent } from './skill-installer.ts';
-import { track } from './telemetry.ts';
-import { CommandError } from './command-result.ts';
-import { addSkillToLock } from './skill-lock.ts';
-import { addSkillToLocalLock, computeSkillFolderHash } from './local-lock.ts';
-import { isSourcePrivate } from './source-parser.ts';
+import { wellKnownProvider } from '../lib/providers/index.ts';
+import { detectInstalledAgents } from '../lib/agents/index.ts';
+import { isSkillInstalled, installWellKnownSkillForAgent } from '../lib/install/index.ts';
+import { track } from '../lib/telemetry.ts';
+import { CommandError } from '../lib/command-result.ts';
+import { addSkillToLock } from '../lib/lock/index.ts';
+import { addSkillToLocalLock, computeSkillFolderHash } from '../lib/lock/index.ts';
+import { isSourcePrivate } from '../lib/parsers/index.ts';
 import { multiselect } from './add-agents.ts';
 
 // --- Helpers ---

src/add-wellknown.ts → src/add/add-wellknown.ts

@@ -1,18 +1,18 @@
 import * as p from '@clack/prompts';
 import pc from 'picocolors';
-import { isSourcePrivate } from './source-parser.ts';
-import { shortenPath, formatList } from './utils.ts';
-import { getCanonicalPath, installWellKnownSkillForAgent } from './skill-installer.ts';
-import { agents } from './agents.ts';
-import { track } from './telemetry.ts';
-import { wellKnownProvider, type WellKnownSkill } from './providers/index.ts';
-import { addSkillToLock } from './skill-lock.ts';
-import { addSkillToLocalLock, computeSkillFolderHash } from './local-lock.ts';
-import type { AgentType } from './types.ts';
+import { isSourcePrivate } from '../lib/parsers/index.ts';
+import { shortenPath, formatList } from '../lib/utils.ts';
+import { getCanonicalPath, installWellKnownSkillForAgent } from '../lib/install/index.ts';
+import { agents } from '../lib/agents/index.ts';
+import { track } from '../lib/telemetry.ts';
+import { wellKnownProvider, type WellKnownSkill } from '../lib/providers/index.ts';
+import { addSkillToLock } from '../lib/lock/index.ts';
+import { addSkillToLocalLock, computeSkillFolderHash } from '../lib/lock/index.ts';
+import type { AgentType } from '../lib/types.ts';
 import { buildAgentSummaryLines } from './add-display.ts';
 import type { AddOptions } from './add-options.ts';
 import { multiselect } from './add-agents.ts';
-import { CommandError } from './command-result.ts';
+import { CommandError } from '../lib/command-result.ts';
 import {
   resolveInstallTargets,
   checkOverwrites,

src/add.test.ts → src/add/add.test.ts

@@ -2,8 +2,8 @@ import { describe, it, expect, beforeEach, afterEach, vi } from 'vitest';
 import { existsSync, rmSync, mkdirSync, writeFileSync } from 'fs';
 import { join } from 'path';
 import { tmpdir } from 'os';
-import { runCli } from './test-utils.ts';
-import { shouldInstallInternalSkills } from './skill-discovery.ts';
+import { runCli } from '../lib/test-utils.ts';
+import { shouldInstallInternalSkills } from '../lib/discovery/index.ts';
 import { parseAddOptions } from './add.ts';
 
 describe('add command', () => {

src/add.ts → src/add/add.ts

@@ -2,31 +2,40 @@ import * as p from '@clack/prompts';
 import pc from 'picocolors';
 import { existsSync } from 'fs';
 import { sep } from 'path';
-import { parseSource, getOwnerRepo, parseOwnerRepo, isRepoPrivate } from './source-parser.ts';
-import { shortenPath, formatList, kebabToTitle } from './utils.ts';
+import { parseSource, getOwnerRepo, parseOwnerRepo, isRepoPrivate } from '../lib/parsers/index.ts';
+import { shortenPath, formatList, kebabToTitle } from '../lib/utils.ts';
 import { multiselect } from './add-agents.ts';
 export { promptForAgents } from './add-agents.ts';
-import { cloneRepo, cleanupTempDir, GitCloneError } from './git.ts';
-import { CommandError } from './command-result.ts';
-import { addPrompts, addAgents, addInstructions, resolveTargetAgents } from './context-add.ts';
-import { TARGET_AGENTS } from './target-agents.ts';
-import { discoverSkills, getSkillDisplayName, filterSkills } from './skill-discovery.ts';
-import { discover } from './context-discovery.ts';
-import { installSkillForAgent, isSkillInstalled, getCanonicalPath } from './skill-installer.ts';
-import { agents } from './agents.ts';
-import { track, setVersion, fetchAuditData } from './telemetry.ts';
+import { cloneRepo, cleanupTempDir, GitCloneError } from '../lib/git/index.ts';
+import { CommandError } from '../lib/command-result.ts';
+import {
+  addPrompts,
+  addAgents,
+  addInstructions,
+  resolveTargetAgents,
+} from '../lib/install/index.ts';
+import { TARGET_AGENTS } from '../lib/agents/index.ts';
+import {
+  discoverSkills,
+  getSkillDisplayName,
+  filterSkills,
+  discover,
+} from '../lib/discovery/index.ts';
+import { installSkillForAgent, isSkillInstalled, getCanonicalPath } from '../lib/install/index.ts';
+import { agents } from '../lib/agents/index.ts';
+import { track, setVersion, fetchAuditData } from '../lib/telemetry.ts';
 import { handleWellKnownSkills } from './add-wellknown.ts';
 import {
   addSkillToLock,
   fetchSkillFolderHash,
   isPromptDismissed,
   dismissPrompt,
-} from './skill-lock.ts';
-import { addSkillToLocalLock, computeSkillFolderHash } from './local-lock.ts';
-import type { Skill, AgentType, TargetAgent, ContextType } from './types.ts';
+} from '../lib/lock/index.ts';
+import { addSkillToLocalLock, computeSkillFolderHash } from '../lib/lock/index.ts';
+import type { Skill, AgentType, TargetAgent, ContextType } from '../lib/types.ts';
 import { parseAddOptions, type AddOptions } from './add-options.ts';
 export { parseAddOptions, type AddOptions } from './add-options.ts';
-import packageJson from '../package.json' with { type: 'json' };
+import packageJson from '../../package.json' with { type: 'json' };
 import { buildSecurityLines, buildAgentSummaryLines } from './add-display.ts';
 import {
   resolveInstallTargets,

src/add/index.ts

@@ -0,0 +1,3 @@
+export { runAdd, initTelemetry } from './add.ts';
+export { parseAddOptions, type AddOptions } from './add-options.ts';
+export { promptForAgents } from './add-agents.ts';

src/check.test.ts → src/check/check.test.ts

@@ -1,17 +1,17 @@
 import { describe, it, expect, vi, beforeEach } from 'vitest';
 import { findSkillUpdates } from './check.ts';
-import type { SkillLockEntry } from './skill-lock.ts';
+import type { SkillLockEntry } from '../lib/lock/index.ts';
 
 // Mock fetchSkillFolderHash from skill-lock.ts
-vi.mock('./skill-lock.ts', async (importOriginal) => {
-  const original = await importOriginal<typeof import('./skill-lock.ts')>();
+vi.mock('../lib/lock/skill-lock.ts', async (importOriginal) => {
+  const original = await importOriginal<typeof import('../lib/lock/skill-lock.ts')>();
   return {
     ...original,
     fetchSkillFolderHash: vi.fn(),
   };
 });
 
-import { fetchSkillFolderHash } from './skill-lock.ts';
+import { fetchSkillFolderHash } from '../lib/lock/index.ts';
 const mockFetch = vi.mocked(fetchSkillFolderHash);
 
 function makeEntry(overrides: Partial<SkillLockEntry> = {}): SkillLockEntry {