trinity-method-sdk 2.0.9 → 2.2.0

package/dist/cli/commands/deploy/agents.js

@@ -42,7 +42,7 @@ export async function deployAgents(templatesPath, variables, spinner) {
     ];
     for (const { dir, agents } of agentDirs) {
         for (const agent of agents) {
-            const templatePath = path.join(templatesPath, 'agents', dir, `${agent}.template`);
+            const templatePath = path.join(templatesPath, '.claude/agents', dir, `${agent}.template`);
             if (await fs.pathExists(templatePath)) {
                 const content = await fs.readFile(templatePath, 'utf8');
                 const processed = processTemplate(content, variables);

package/dist/cli/commands/deploy/ci-cd.d.ts

@@ -1,13 +1,14 @@
 /**
- * CI/CD workflow deployment
+ * CI workflow deployment
  */
 import type { DeployOptions, Spinner } from './types.js';
 /**
- * Deploy CI/CD workflow templates
+ * Deploy CI workflow templates
  *
  * @param options - Deploy command options
  * @param spinner - Spinner instance for status updates
+ * @param variables - Template variables for processing
  * @returns Number of files deployed
  */
-export declare function deployCICD(options: DeployOptions, spinner: Spinner): Promise<number>;
+export declare function deployCICD(options: DeployOptions, spinner: Spinner, variables?: Record<string, string>): Promise<number>;
 //# sourceMappingURL=ci-cd.d.ts.map

package/dist/cli/commands/deploy/ci-cd.js

@@ -1,30 +1,31 @@
 /**
- * CI/CD workflow deployment
+ * CI workflow deployment
  */
 import chalk from 'chalk';
 import { deployCITemplates } from '../../utils/deploy-ci.js';
 /**
- * Deploy CI/CD workflow templates
+ * Deploy CI workflow templates
  *
  * @param options - Deploy command options
  * @param spinner - Spinner instance for status updates
+ * @param variables - Template variables for processing
  * @returns Number of files deployed
  */
-export async function deployCICD(options, spinner) {
+export async function deployCICD(options, spinner, variables = {}) {
     if (!options.ciDeploy) {
         return 0;
     }
-    spinner.start('Deploying CI/CD workflow templates...');
+    spinner.start('Deploying CI workflow templates...');
     try {
-        const ciStats = await deployCITemplates(options);
+        const ciStats = await deployCITemplates(options, variables);
         if (ciStats.deployed.length > 0) {
-            spinner.succeed(`CI/CD templates deployed (${ciStats.deployed.length} files)`);
+            spinner.succeed(`CI templates deployed (${ciStats.deployed.length} files)`);
             ciStats.deployed.forEach((file) => {
                 console.log(chalk.white(`   ✓ ${file}`));
             });
         }
         else {
-            spinner.info('No CI/CD templates deployed');
+            spinner.info('No CI templates deployed');
         }
         if (ciStats.skipped.length > 0) {
             console.log(chalk.yellow('   Skipped:'));
@@ -33,7 +34,7 @@ export async function deployCICD(options, spinner) {
             });
         }
         if (ciStats.errors.length > 0) {
-            spinner.warn('Some CI/CD templates failed to deploy');
+            spinner.warn('Some CI templates failed to deploy');
             ciStats.errors.forEach((err) => {
                 console.log(chalk.red(`   ✗ ${err.file || 'Error'}: ${err.error}`));
             });
@@ -41,7 +42,7 @@ export async function deployCICD(options, spinner) {
         return ciStats.deployed.length;
     }
     catch (error) {
-        spinner.fail('CI/CD template deployment failed');
+        spinner.fail('CI template deployment failed');
         const { displayWarning, getErrorMessage } = await import('../../utils/errors.js');
         displayWarning(getErrorMessage(error));
         return 0;

package/dist/cli/commands/deploy/claude-setup.js

@@ -26,7 +26,7 @@ export async function deployClaudeSetup(templatesPath, variables, spinner) {
     spinner.succeed('Claude Code settings created (empty - customize as needed)');
     // Deploy Employee Directory
     spinner.start('Deploying Employee Directory...');
-    const employeeDirectoryTemplate = path.join(templatesPath, 'claude', 'EMPLOYEE-DIRECTORY.md.template');
+    const employeeDirectoryTemplate = path.join(templatesPath, '.claude', 'EMPLOYEE-DIRECTORY.md.template');
     if (await fs.pathExists(employeeDirectoryTemplate)) {
         const content = await fs.readFile(employeeDirectoryTemplate, 'utf8');
         const processed = processTemplate(content, variables);
@@ -48,41 +48,34 @@ export async function deployClaudeSetup(templatesPath, variables, spinner) {
     await fs.ensureDir(`${commandsDir}/execution`);
     await fs.ensureDir(`${commandsDir}/investigation`);
     await fs.ensureDir(`${commandsDir}/infrastructure`);
+    await fs.ensureDir(`${commandsDir}/maintenance`);
     await fs.ensureDir(`${commandsDir}/utility`);
-    // Command categorization map
-    const commandCategories = {
-        'trinity-start.md.template': 'session',
-        'trinity-continue.md.template': 'session',
-        'trinity-end.md.template': 'session',
-        'trinity-requirements.md.template': 'planning',
-        'trinity-design.md.template': 'planning',
-        'trinity-decompose.md.template': 'planning',
-        'trinity-plan.md.template': 'planning',
-        'trinity-orchestrate.md.template': 'execution',
-        'trinity-audit.md.template': 'execution',
-        'trinity-readme.md.template': 'execution',
-        'trinity-docs.md.template': 'execution',
-        'trinity-changelog.md.template': 'execution',
-        'trinity-create-investigation.md.template': 'investigation',
-        'trinity-plan-investigation.md.template': 'investigation',
-        'trinity-investigate-templates.md.template': 'investigation',
-        'trinity-init.md.template': 'infrastructure',
-        'trinity-agents.md.template': 'utility',
-        'trinity-verify.md.template': 'utility',
-        'trinity-workorder.md.template': 'utility',
-    };
-    const commandsTemplatePath = path.join(templatesPath, 'shared/claude-commands');
-    const commandFiles = await fs.readdir(commandsTemplatePath);
-    for (const file of commandFiles) {
-        if (file.endsWith('.md.template') && commandCategories[file]) {
-            const sourcePath = path.join(commandsTemplatePath, file);
-            const category = commandCategories[file];
-            // Remove .template extension for deployed files
-            const deployedName = file.replace('.template', '');
-            const destPath = path.join(commandsDir, category, deployedName);
-            await fs.copy(sourcePath, destPath);
-            commandsDeployed++;
-            filesDeployed++;
+    // Commands are now organized by category in source templates
+    const commandsTemplatePath = path.join(templatesPath, '.claude/commands');
+    const categories = [
+        'session',
+        'planning',
+        'execution',
+        'investigation',
+        'infrastructure',
+        'maintenance',
+        'utility',
+    ];
+    for (const category of categories) {
+        const categoryPath = path.join(commandsTemplatePath, category);
+        if (await fs.pathExists(categoryPath)) {
+            const commandFiles = await fs.readdir(categoryPath);
+            for (const file of commandFiles) {
+                if (file.endsWith('.md.template')) {
+                    const sourcePath = path.join(categoryPath, file);
+                    // Remove .template extension for deployed files
+                    const deployedName = file.replace('.template', '');
+                    const destPath = path.join(commandsDir, category, deployedName);
+                    await fs.copy(sourcePath, destPath);
+                    commandsDeployed++;
+                    filesDeployed++;
+                }
+            }
         }
     }
     spinner.succeed(`Deployed ${commandsDeployed} Trinity slash commands (6 categories)`);

package/dist/cli/commands/deploy/configuration.js

@@ -66,7 +66,7 @@ async function promptLintingChoice(stack) {
         {
             type: 'confirm',
             name: 'setupLinting',
-            message: 'Setup linting configuration? (y/n)',
+            message: 'Setup linting configuration?',
             default: true,
         },
     ]);
@@ -82,7 +82,6 @@ async function promptLintingChoice(stack) {
  */
 async function configureRecommendedLinting(stack) {
     const tools = getRecommendedTools(stack.framework, stack.language);
-    console.log(chalk.green('\n✔ Setup linting configuration?'), 'Recommended\n');
     const dependencies = getDependenciesForTools(tools);
     const scripts = getScriptsForTools(tools);
     displayLintingConfig(tools, dependencies, scripts);
@@ -111,35 +110,35 @@ async function detectGitPlatform() {
  * Display CI/CD configuration summary
  */
 function displayCICDConfig(platform) {
-    console.log(chalk.green('\n✔ Deploy CI/CD workflow templates?'), 'Yes');
+    console.log(chalk.green('\n✔ Deploy CI workflow templates?'), 'yes');
     if (platform !== 'unknown') {
         console.log(chalk.cyan(`📦 Detected platform: ${platform}\n`));
         console.log(chalk.white('  Will configure:'));
         if (platform === 'GitHub Actions') {
-            console.log(chalk.white('  ✓ .github/workflows/trinity-ci.yml'));
+            console.log(chalk.white('  ✓ .github/workflows/ci.yml'));
         }
         else if (platform === 'GitLab CI') {
             console.log(chalk.white('  ✓ .gitlab-ci.yml'));
         }
-        console.log(chalk.white('  ✓ trinity/templates/ci/generic-ci.yml (reference)'));
+        console.log(chalk.white('  ✓ .claude/trinity/templates/ci/generic-ci.yml (reference)'));
     }
     else {
         console.log(chalk.cyan('\n📦 Will configure:\n'));
-        console.log(chalk.white('  ✓ .github/workflows/trinity-ci.yml (GitHub Actions)'));
-        console.log(chalk.white('  ✓ trinity/templates/ci/generic-ci.yml (reference)'));
+        console.log(chalk.white('  ✓ .github/workflows/ci.yml (GitHub Actions)'));
+        console.log(chalk.white('  ✓ .claude/trinity/templates/ci/generic-ci.yml (reference)'));
     }
 }
 /**
  * Prompt for CI/CD setup
  */
 async function promptCICDSetup() {
-    console.log(chalk.cyan('\n⚙️  Optional: CI/CD Automation\n'));
-    console.log(chalk.white('Trinity can setup automated testing workflows for your CI/CD platform.\n'));
+    console.log(chalk.cyan('\n⚙️  Optional: CI Automation\n'));
+    console.log(chalk.white('Trinity can setup automated testing workflows for your CI platform.\n'));
     const ciChoice = await inquirer.prompt([
         {
             type: 'confirm',
             name: 'setupCI',
-            message: 'Deploy CI/CD workflow templates?',
+            message: 'Deploy CI workflow templates?',
             default: true,
         },
     ]);
@@ -149,7 +148,7 @@ async function promptCICDSetup() {
         return true;
     }
     else {
-        console.log(chalk.gray('\n✔ Deploy CI/CD workflow templates?'), 'Skip\n');
+        console.log(chalk.gray('\n✔ Deploy CI workflow templates?'), 'Skip\n');
         return false;
     }
 }

package/dist/cli/commands/deploy/directories.js

@@ -11,20 +11,19 @@ import fs from 'fs-extra';
 export async function createDirectories(spinner) {
     spinner.start('Creating Trinity Method structure...');
     let directoriesCreated = 0;
-    // Trinity core directories
-    await fs.ensureDir('trinity/knowledge-base');
-    await fs.ensureDir('trinity/sessions');
-    await fs.ensureDir('trinity/investigations');
-    await fs.ensureDir('trinity/patterns');
-    await fs.ensureDir('trinity/work-orders');
-    await fs.ensureDir('trinity/templates');
-    await fs.ensureDir('trinity/reports');
-    await fs.ensureDir('trinity/investigations/plans');
-    await fs.ensureDir('trinity/archive/work-orders');
-    await fs.ensureDir('trinity/archive/investigations');
-    await fs.ensureDir('trinity/archive/reports');
-    await fs.ensureDir('trinity/archive/sessions');
-    directoriesCreated += 12;
+    // Trinity core directories (inside .claude/)
+    await fs.ensureDir('.claude/trinity/knowledge-base');
+    await fs.ensureDir('.claude/trinity/sessions');
+    await fs.ensureDir('.claude/trinity/investigations');
+    await fs.ensureDir('.claude/trinity/work-orders');
+    await fs.ensureDir('.claude/trinity/templates');
+    await fs.ensureDir('.claude/trinity/reports');
+    await fs.ensureDir('.claude/trinity/investigations/plans');
+    await fs.ensureDir('.claude/trinity/archive/work-orders');
+    await fs.ensureDir('.claude/trinity/archive/investigations');
+    await fs.ensureDir('.claude/trinity/archive/reports');
+    await fs.ensureDir('.claude/trinity/archive/sessions');
+    directoriesCreated += 11;
     // Claude Code directories
     await fs.ensureDir('.claude/agents/leadership');
     await fs.ensureDir('.claude/agents/deployment');

package/dist/cli/commands/deploy/gitignore.js

@@ -18,14 +18,12 @@ export async function updateGitignore(spinner) {
         if (await fs.pathExists(gitignorePath)) {
             gitignoreContent = await fs.readFile(gitignorePath, 'utf8');
         }
-        // Trinity files to ignore
+        // Trinity files to ignore (archive and templates are ephemeral/generated)
         const trinityIgnores = [
             '',
             '# Trinity Method SDK',
-            '.claude/',
-            'trinity/',
-            '*CLAUDE.md',
-            'TRINITY.md',
+            '.claude/trinity/archive/',
+            '.claude/trinity/templates/',
         ];
         // Check if Trinity section already exists
         if (!gitignoreContent.includes('# Trinity Method SDK')) {

package/dist/cli/commands/deploy/index.d.ts

@@ -13,7 +13,7 @@
  * Manual setup is error-prone and inconsistent. Developers forget folders, skip quality tools, or
  * misconfigure agents. This command orchestrates TAN (structure), ZEN (documentation), INO (context),
  * and EIN (CI/CD) to deploy battle-tested Trinity infrastructure in minutes. Every project gets same
- * high-quality foundation: 19 agents, 20 commands, quality gates, and documentation architecture.
+ * high-quality foundation: 18 agents, 20 commands, quality gates, and documentation architecture.
  *
  * @example
  * ```bash

package/dist/cli/commands/deploy/index.js

@@ -13,7 +13,7 @@
  * Manual setup is error-prone and inconsistent. Developers forget folders, skip quality tools, or
  * misconfigure agents. This command orchestrates TAN (structure), ZEN (documentation), INO (context),
  * and EIN (CI/CD) to deploy battle-tested Trinity infrastructure in minutes. Every project gets same
- * high-quality foundation: 19 agents, 20 commands, quality gates, and documentation architecture.
+ * high-quality foundation: 18 agents, 20 commands, quality gates, and documentation architecture.
  *
  * @example
  * ```bash
@@ -75,6 +75,10 @@ export async function deploy(options) {
         spinner.succeed(`Detected: ${stack.framework} (${stack.language}) - Source: ${stack.sourceDir}`);
         // STEP 3: Interactive configuration (or use defaults with --yes)
         const config = await promptConfiguration(options, stack);
+        // Bridge interactive CI/CD selection to deployment flag
+        if (config.enableCICD) {
+            options.ciDeploy = true;
+        }
         // STEP 3.5: Collect codebase metrics
         let metrics;
         if (!options.skipAudit) {
@@ -98,7 +102,7 @@ export async function deploy(options) {
             PACKAGE_MANAGER: stack.packageManager || 'npm',
             BACKEND_FRAMEWORK: stack.framework,
             CURRENT_DATE: new Date().toISOString(),
-            TRINITY_VERSION: pkg.version || '2.0.9',
+            TRINITY_VERSION: pkg.version || '2.1.0',
         };
         // STEP 4: Create directory structure
         const directoriesCreated = await createDirectories(spinner);
@@ -126,7 +130,7 @@ export async function deploy(options) {
         const templatesDeployed = await deployTemplates(templatesPath, variables, spinner);
         progress.templatesDeployed = templatesDeployed;
         // STEP 11: Deploy CI/CD workflow templates (if enabled)
-        const cicdFiles = await deployCICD(options, spinner);
+        const cicdFiles = await deployCICD(options, spinner, variables);
         progress.rootFilesDeployed += cicdFiles;
         // STEP 11.5: Update .gitignore
         const gitignoreUpdated = await updateGitignore(spinner);

package/dist/cli/commands/deploy/knowledge-base.js

@@ -30,12 +30,12 @@ export async function deployKnowledgeBase(templatesPath, variables, stack, metri
         'DOCUMENTATION-CRITERIA.md',
     ];
     for (const template of kbTemplates) {
-        const templatePath = path.join(templatesPath, 'knowledge-base', `${template}.template`);
+        const templatePath = path.join(templatesPath, 'trinity/knowledge-base', `${template}.template`);
         if (await fs.pathExists(templatePath)) {
             const content = await fs.readFile(templatePath, 'utf8');
             const processed = processTemplate(content, variables);
             // Validate destination path for security
-            const destPath = validatePath(`trinity/knowledge-base/${template}`);
+            const destPath = validatePath(`.claude/trinity/knowledge-base/${template}`);
             await fs.writeFile(destPath, processed);
             filesDeployed++;
         }
@@ -44,7 +44,7 @@ export async function deployKnowledgeBase(templatesPath, variables, stack, metri
     // Enrich knowledge base with project metrics
     try {
         spinner.start('Enriching knowledge base with project metrics...');
-        const archPath = 'trinity/knowledge-base/ARCHITECTURE.md';
+        const archPath = '.claude/trinity/knowledge-base/ARCHITECTURE.md';
         if (await fs.pathExists(archPath)) {
             let archContent = await fs.readFile(archPath, 'utf8');
             // Replace common placeholders with actual data

package/dist/cli/commands/deploy/pre-flight.js

@@ -13,7 +13,7 @@ import chalk from 'chalk';
 export async function checkPreFlight(options, spinner) {
     spinner.start('Running pre-flight checks...');
     // Check if Trinity is already deployed
-    const trinityExists = await fs.pathExists('trinity');
+    const trinityExists = await fs.pathExists('.claude/trinity');
     if (trinityExists && !options.force) {
         spinner.fail();
         console.log(chalk.yellow('\nTrinity Method is already deployed in this project.'));

package/dist/cli/commands/deploy/root-files.js

@@ -6,20 +6,6 @@ import path from 'path';
 import chalk from 'chalk';
 import { processTemplate } from '../../utils/template-processor.js';
 import { validatePath } from '../../utils/validate-path.js';
-/**
- * Deploy TRINITY.md root file
- */
-async function deployTrinityMarkdown(templatesPath, variables) {
-    const trinityRootTemplate = path.join(templatesPath, 'root', 'TRINITY.md.template');
-    if (await fs.pathExists(trinityRootTemplate)) {
-        const content = await fs.readFile(trinityRootTemplate, 'utf8');
-        const processed = processTemplate(content, variables);
-        const destPath = validatePath('TRINITY.md');
-        await fs.writeFile(destPath, processed);
-        return 1;
-    }
-    return 0;
-}
 /**
  * Deploy root CLAUDE.md file
  */
@@ -38,8 +24,8 @@ async function deployRootClaudeMarkdown(templatesPath, variables) {
  * Deploy VERSION file
  */
 async function deployVersionFile(pkgVersion) {
-    const versionPath = validatePath('trinity/VERSION');
-    await fs.writeFile(versionPath, pkgVersion || '2.0.9');
+    const versionPath = validatePath('.claude/trinity/VERSION');
+    await fs.writeFile(versionPath, pkgVersion || '2.1.0');
     return 1;
 }
 /**
@@ -51,7 +37,7 @@ async function deployTrinityClaudeMarkdown(templatesPath, variables, spinner) {
     if (await fs.pathExists(trinityCLAUDETemplate)) {
         const content = await fs.readFile(trinityCLAUDETemplate, 'utf8');
         const processed = processTemplate(content, variables);
-        const destPath = validatePath('trinity/CLAUDE.md');
+        const destPath = validatePath('.claude/trinity/CLAUDE.md');
         await fs.writeFile(destPath, processed);
         spinner.succeed('Trinity CLAUDE.md deployed');
         return 1;
@@ -163,7 +149,6 @@ export async function deployRootFiles(templatesPath, variables, stack, pkgVersio
     let filesDeployed = 0;
     // Deploy root files
     spinner.start('Creating root files...');
-    filesDeployed += await deployTrinityMarkdown(templatesPath, variables);
     filesDeployed += await deployRootClaudeMarkdown(templatesPath, variables);
     filesDeployed += await deployVersionFile(pkgVersion);
     spinner.succeed('Root files created');

package/dist/cli/commands/deploy/sdk-install.js

@@ -24,7 +24,7 @@ export async function installSDK(spinner) {
                 if (!packageJson.dependencies) {
                     packageJson.dependencies = {};
                 }
-                packageJson.dependencies['trinity-method-sdk'] = '^2.0.9';
+                packageJson.dependencies['trinity-method-sdk'] = '^2.1.0';
                 await fs.writeJson(packageJsonPath, packageJson, { spaces: 2 });
                 spinner.text = 'Installing Trinity Method SDK (this may take a moment)...';
                 // Install dependencies

package/dist/cli/commands/deploy/summary.js

@@ -6,7 +6,7 @@ import chalk from 'chalk';
 /**
  * Display deployment statistics section
  */
-function displayStatistics(stats, stack, claudeMdCount, claudeMdSummary) {
+function displayStatistics(stats, _stack, claudeMdCount, claudeMdSummary) {
     console.log(chalk.cyan('📊 Deployment Statistics (v2.0):\n'));
     console.log(chalk.white(`   Directories Created: ${stats.directories || 17}`));
     console.log(chalk.white(`   Agents Deployed: ${stats.agentsDeployed} (v2.0: 2 leadership + 4 planning + 7 execution + 4 deployment + 1 audit)`));
@@ -88,8 +88,8 @@ function displayNextSteps(options, stack) {
         step++;
     }
     // Standard next steps
-    console.log(chalk.white(`   ${step}. Review trinity/knowledge-base/ARCHITECTURE.md`));
-    console.log(chalk.white(`   ${step + 1}. Update trinity/knowledge-base/To-do.md`));
+    console.log(chalk.white(`   ${step}. Review .claude/trinity/knowledge-base/ARCHITECTURE.md`));
+    console.log(chalk.white(`   ${step + 1}. Update .claude/trinity/knowledge-base/To-do.md`));
     console.log(chalk.white(`   ${step + 2}. Open Claude Code and start your first Trinity session`));
     console.log(chalk.white(`   ${step + 3}. Agents will be automatically invoked as needed\n`));
     // Test linting command (if applicable)

package/dist/cli/commands/deploy/templates.js

@@ -25,15 +25,15 @@ export async function deployTemplates(templatesPath, variables, spinner) {
         'PATTERN-TEMPLATE.md.template',
         'VERIFICATION-TEMPLATE.md.template',
     ];
-    await fs.ensureDir('trinity/templates/work-orders');
+    await fs.ensureDir('.claude/trinity/templates/work-orders');
     for (const template of woTemplates) {
-        const templatePath = path.join(templatesPath, 'work-orders', template);
+        const templatePath = path.join(templatesPath, 'trinity/templates/work-orders', template);
         if (await fs.pathExists(templatePath)) {
             const content = await fs.readFile(templatePath, 'utf8');
             const processed = processTemplate(content, variables);
             const deployedName = template.replace('.template', '');
             // Validate destination path for security
-            const destPath = validatePath(`trinity/templates/work-orders/${deployedName}`);
+            const destPath = validatePath(`.claude/trinity/templates/work-orders/${deployedName}`);
             await fs.writeFile(destPath, processed);
             templatesDeployed++;
         }
@@ -48,37 +48,50 @@ export async function deployTemplates(templatesPath, variables, spinner) {
         'security.md.template',
         'technical.md.template',
     ];
-    await fs.ensureDir('trinity/templates/investigations');
+    await fs.ensureDir('.claude/trinity/templates/investigations');
     for (const template of investigationTemplates) {
-        const templatePath = path.join(templatesPath, 'investigations', template);
+        const templatePath = path.join(templatesPath, 'trinity/templates/investigations', template);
         if (await fs.pathExists(templatePath)) {
             const content = await fs.readFile(templatePath, 'utf8');
             const processed = processTemplate(content, variables);
             const deployedName = template.replace('.template', '');
             // Validate destination path for security
-            const destPath = validatePath(`trinity/templates/investigations/${deployedName}`);
+            const destPath = validatePath(`.claude/trinity/templates/investigations/${deployedName}`);
             await fs.writeFile(destPath, processed);
             templatesDeployed++;
         }
     }
     spinner.succeed(`Investigation templates deployed (${investigationTemplates.length} templates)`);
-    // Deploy documentation templates
+    // Deploy documentation templates (all 28 templates including subdirectories)
     spinner.start('Deploying documentation templates...');
-    const documentationTemplates = ['ROOT-README.md.template', 'SUBDIRECTORY-README.md.template'];
-    await fs.ensureDir('trinity/templates/documentation');
-    for (const template of documentationTemplates) {
-        const templatePath = path.join(templatesPath, 'documentation', template);
-        if (await fs.pathExists(templatePath)) {
-            const content = await fs.readFile(templatePath, 'utf8');
-            const processed = processTemplate(content, variables);
-            const deployedName = template.replace('.template', '');
-            // Validate destination path for security
-            const destPath = validatePath(`trinity/templates/documentation/${deployedName}`);
-            await fs.writeFile(destPath, processed);
-            templatesDeployed++;
+    const docSourcePath = path.join(templatesPath, 'trinity/templates/documentation');
+    const docDestPath = '.claude/trinity/templates/documentation';
+    await fs.ensureDir(docDestPath);
+    // Recursively copy all documentation templates, removing .template extension
+    async function copyDocTemplates(sourcePath, destPath) {
+        const items = await fs.readdir(sourcePath);
+        for (const item of items) {
+            const sourceItemPath = path.join(sourcePath, item);
+            const stat = await fs.stat(sourceItemPath);
+            if (stat.isDirectory()) {
+                // Create subdirectory and recurse
+                const destSubDir = path.join(destPath, item);
+                await fs.ensureDir(destSubDir);
+                await copyDocTemplates(sourceItemPath, destSubDir);
+            }
+            else if (item.endsWith('.md.template')) {
+                // Process template file and remove .template extension
+                const content = await fs.readFile(sourceItemPath, 'utf8');
+                const processed = processTemplate(content, variables);
+                const deployedName = item.replace('.template', '');
+                const destFilePath = validatePath(path.join(destPath, deployedName));
+                await fs.writeFile(destFilePath, processed);
+                templatesDeployed++;
+            }
         }
     }
-    spinner.succeed(`Documentation templates deployed (${documentationTemplates.length} templates)`);
+    await copyDocTemplates(docSourcePath, docDestPath);
+    spinner.succeed(`Documentation templates deployed (${templatesDeployed - 11} templates)`);
     return templatesDeployed;
 }
 //# sourceMappingURL=templates.js.map

package/dist/cli/commands/update/agents.js

@@ -16,7 +16,7 @@ const AGENT_DIRS = ['leadership', 'planning', 'aj-team', 'deployment', 'audit'];
 export async function updateAgents(spinner, stats) {
     spinner.start('Updating agents...');
     const sdkPath = await getSDKPath();
-    const agentsTemplatePath = path.join(sdkPath, 'dist/templates/agents');
+    const agentsTemplatePath = path.join(sdkPath, 'dist/templates/.claude/agents');
     for (const agentDir of AGENT_DIRS) {
         const sourcePath = path.join(agentsTemplatePath, agentDir);
         const targetPath = path.join('.claude/agents', agentDir);

package/dist/cli/commands/update/backup.js

@@ -7,10 +7,10 @@ import fs from 'fs-extra';
 import path from 'path';
 /** User-managed files that need backup */
 const USER_FILES = [
-    'trinity/knowledge-base/ARCHITECTURE.md',
-    'trinity/knowledge-base/To-do.md',
-    'trinity/knowledge-base/ISSUES.md',
-    'trinity/knowledge-base/Technical-Debt.md',
+    '.claude/trinity/knowledge-base/ARCHITECTURE.md',
+    '.claude/trinity/knowledge-base/To-do.md',
+    '.claude/trinity/knowledge-base/ISSUES.md',
+    '.claude/trinity/knowledge-base/Technical-Debt.md',
 ];
 /**
  * Create backup of Trinity Method files before update
@@ -28,8 +28,7 @@ export async function createUpdateBackup(spinner) {
             await fs.copy(file, backupPath);
         }
     }
-    // Backup entire trinity and .claude dirs for rollback safety
-    await fs.copy('trinity', path.join(backupDir, 'trinity'));
+    // Backup entire .claude dir for rollback safety (includes .claude/trinity/)
     await fs.copy('.claude', path.join(backupDir, '.claude'));
     spinner.succeed('Backup created');
     return backupDir;
@@ -60,12 +59,7 @@ export async function rollbackFromBackup(backupDir) {
     }
     const rollbackSpinner = await import('ora').then((m) => m.default('Restoring from backup...').start());
     try {
-        // Restore trinity directory
-        if (await fs.pathExists(path.join(backupDir, 'trinity'))) {
-            await fs.remove('trinity');
-            await fs.copy(path.join(backupDir, 'trinity'), 'trinity');
-        }
-        // Restore .claude directory
+        // Restore .claude directory (includes .claude/trinity/)
         if (await fs.pathExists(path.join(backupDir, '.claude'))) {
             await fs.remove('.claude');
             await fs.copy(path.join(backupDir, '.claude'), '.claude');

package/dist/cli/commands/update/commands.d.ts

@@ -7,6 +7,7 @@ import { Ora } from 'ora';
 import { UpdateStats } from './types.js';
 /**
  * Update slash command files from SDK to .claude/commands/
+ * Commands are now organized by category in source templates
  * @param spinner - ora spinner instance for status display
  * @param stats - update statistics to track progress
  */