@polymorphism-tech/morph-spec 4.3.7 → 4.6.0

package/src/commands/project/update.js

@@ -1,5 +1,7 @@
 import { join, dirname } from 'path';
 import { fileURLToPath } from 'url';
+import { spawnSync } from 'child_process';
+import { existsSync } from 'fs';
 
 const __dirname = dirname(fileURLToPath(import.meta.url));
 import fs from 'fs-extra';
@@ -12,8 +14,6 @@ import {
   copyFile,
   pathExists,
   ensureDir,
-  createDirectoryLink,
-  createSymlink,
   readJson,
   writeJson
 } from '../../utils/file-copier.js';
@@ -24,7 +24,9 @@ import {
   getUpdateInstructions,
   detectInstallMethod
 } from '../../utils/version-checker.js';
-import { installClaudeHooks } from '../../utils/hooks-installer.js';
+import { installClaudeHooks } from '../../utils/claude-settings-manager.js';
+import { installSkills } from '../../utils/skills-installer.js';
+import { installAgents, installDomainAgents } from '../../utils/agents-installer.js';
 import { AutoContextOrchestrator } from '../../core/orchestrator.js';
 import { detectClaudeCode } from '../../llm/environment-detector.js';
 
@@ -53,8 +55,8 @@ async function backupUserConfig(morphPath) {
  */
 async function cleanFrameworkDirs(morphPath, targetPath) {
   const dirsToClean = [
-    join(morphPath, 'templates'),
-    join(morphPath, 'standards'),
+    join(morphPath, 'framework', 'templates'),
+    join(morphPath, 'framework', 'standards'),
     join(morphPath, 'config'),
     join(targetPath, '.claude')
   ];
@@ -115,9 +117,9 @@ export async function updateCommand(options) {
     needsInitialization = true;
 
     // Create basic .morph structure
-    await ensureDir(join(morphPath, 'project', 'context'));
-    await ensureDir(join(morphPath, 'project', 'standards'));
-    await ensureDir(join(morphPath, 'project', 'outputs'));
+    await ensureDir(join(morphPath, 'context'));
+    await ensureDir(join(morphPath, 'features'));
+    await ensureDir(join(morphPath, 'framework'));
     await ensureDir(join(morphPath, 'config'));
     logger.dim('  ✓ Created .morph directory structure');
   }
@@ -194,7 +196,7 @@ export async function updateCommand(options) {
     if (updateTemplates) {
       updateSpinner.text = 'Updating templates...';
       const templatesSrc = join(contentDir, 'framework', 'templates');
-      const templatesDest = join(morphPath, 'templates');
+      const templatesDest = join(morphPath, 'framework', 'templates');
       await copyDirectory(templatesSrc, templatesDest);
     }
 
@@ -202,30 +204,31 @@ export async function updateCommand(options) {
     if (updateStandards) {
       updateSpinner.text = 'Updating standards...';
       const standardsSrc = join(contentDir, 'framework', 'standards');
-      const standardsDest = join(morphPath, 'standards');
+      const standardsDest = join(morphPath, 'framework', 'standards');
       await copyDirectory(standardsSrc, standardsDest);
     }
 
     // Update agents.json (sourced from framework/ — canonical single source of truth)
     updateSpinner.text = 'Updating agents configuration...';
     const agentsSrc = join(__dirname, '..', '..', '..', 'framework', 'agents.json');
-    const agentsDest = join(morphPath, 'config', 'agents.json');
+    const agentsDest = join(morphPath, 'framework', 'agents.json');
     if (await pathExists(agentsSrc)) {
       await copyFile(agentsSrc, agentsDest);
     }
 
-    // Update azure-pricing files
-    updateSpinner.text = 'Updating Azure pricing data...';
-    const configDir = join(morphPath, 'config');
-    const pricingSrc = join(contentDir, '.morph', 'config', 'azure-pricing.json');
-    const pricingDest = join(configDir, 'azure-pricing.json');
-    if (await pathExists(pricingSrc)) {
-      await copyFile(pricingSrc, pricingDest);
-    }
-    const pricingSchemaSrc = join(contentDir, '.morph', 'config', 'azure-pricing.schema.json');
-    const pricingSchemaDest = join(configDir, 'azure-pricing.schema.json');
-    if (await pathExists(pricingSchemaSrc)) {
-      await copyFile(pricingSchemaSrc, pricingSchemaDest);
+    // Regenerate derived files (phase-utils.js, skill output tables) from output-schema.js
+    // Only runs when the generator script is present (framework dev installs via npm link)
+    updateSpinner.text = 'Syncing generated refs...';
+    try {
+      const generateScript = join(__dirname, '..', '..', '..', 'scripts', 'generate-refs.js');
+      if (existsSync(generateScript)) {
+        const result = spawnSync(process.execPath, [generateScript], { encoding: 'utf8' });
+        if (result.status === 0) {
+          logger.dim('  ✓ Generated refs synced (phase-utils.js, skill outputs)');
+        }
+      }
+    } catch {
+      // Non-fatal: generator unavailable or files already in sync
     }
 
     // Update .claude commands and skills
@@ -234,8 +237,6 @@ export async function updateCommand(options) {
     const frameworkDir = join(__dirname, '..', '..', '..', 'framework');
     const claudeDest = join(targetPath, '.claude');
 
-    let symlinkCount = 0;
-    let copyCount = 0;
     let commandsCopied = false;
 
     // Copy commands directory (slash commands): framework/commands/ → .claude/commands/
@@ -248,64 +249,40 @@ export async function updateCommand(options) {
       logger.warn('  ⚠ framework/commands/ source missing — commands not updated');
     }
 
-    // Create directory links for skill categories (or copy if linking fails)
-    // Source: framework/skills/ → .claude/skills/
-    {
-      const skillsSrc = join(frameworkDir, 'skills');
-      const skillsDest = join(claudeDest, 'skills');
-
-      if (await pathExists(skillsSrc)) {
-        await ensureDir(skillsDest);
-
-        const entries = await fs.readdir(skillsSrc, { withFileTypes: true });
-
-        let linkedCategories = 0;
-        let copiedCategories = 0;
-        let totalSkillFiles = 0;
-
-        // Link category directories (specialists/, infra/, checklists/, etc.)
-        for (const entry of entries) {
-          if (entry.isDirectory()) {
-            const categorySrc = join(skillsSrc, entry.name);
-            const categoryDest = join(skillsDest, entry.name);
-
-            // Count .md files for reporting
-            const categoryEntries = await fs.readdir(categorySrc, { withFileTypes: true });
-            const mdFiles = categoryEntries.filter(e => e.isFile() && e.name.endsWith('.md'));
-            totalSkillFiles += mdFiles.length;
-
-            const result = await createDirectoryLink(categorySrc, categoryDest);
-            if (result === 'copy') {
-              copiedCategories++;
-            } else {
-              linkedCategories++;
-            }
-          } else if (entry.isFile() && entry.name.endsWith('.md')) {
-            // Handle .md files in skills root
-            totalSkillFiles++;
-            const result = await createSymlink(join(skillsSrc, entry.name), join(skillsDest, entry.name), 'file');
-            if (result === 'symlink') {
-              linkedCategories++;
-            } else {
-              copiedCategories++;
-            }
-          }
-        }
+    // Sync morph skills to .claude/skills/ for native Claude Code discovery
+    updateSpinner.text = 'Syncing morph skills to .claude/skills/...';
+    await installSkills(targetPath);
+
+    // Sync native subagents to .claude/agents/
+    updateSpinner.text = 'Syncing agents to .claude/agents/...';
+    await installAgents(targetPath, frameworkDir);
+    await installDomainAgents(targetPath, frameworkDir);
+
+    // Sync path-scoped rules to .claude/rules/
+    updateSpinner.text = 'Syncing rules to .claude/rules/...';
+    const rulesSrc = join(frameworkDir, 'rules');
+    const rulesDest = join(claudeDest, 'rules');
+    if (await pathExists(rulesSrc)) {
+      await copyDirectory(rulesSrc, rulesDest);
+    }
 
-        symlinkCount = linkedCategories > 0 ? totalSkillFiles : 0;
-        copyCount = linkedCategories === 0 ? totalSkillFiles : 0;
-      }
+    // Sync runtime CLAUDE.md to .claude/CLAUDE.md
+    updateSpinner.text = 'Syncing .claude/CLAUDE.md...';
+    const runtimeSrc = join(frameworkDir, 'CLAUDE.md');
+    const runtimeDest = join(claudeDest, 'CLAUDE.md');
+    if (await pathExists(runtimeSrc)) {
+      await copyFile(runtimeSrc, runtimeDest);
     }
 
-    // Update agent-teams hooks in .claude/settings.local.json
+    // Update Claude Code hooks in .claude/settings.local.json
     updateSpinner.text = 'Updating Claude Code hooks...';
-    await installClaudeHooks(targetPath);
+    const hooksResult = await installClaudeHooks(targetPath);
 
     // Update CLAUDE.md
     updateSpinner.text = 'Updating CLAUDE.md...';
-    const claudeMdSrc = join(contentDir, 'CLAUDE.md');
+    const claudeMdSrc = join(frameworkDir, 'CLAUDE.md');
     const claudeMdDest = join(targetPath, 'CLAUDE.md');
-    await copyDirectory(claudeMdSrc, claudeMdDest);
+    await copyFile(claudeMdSrc, claudeMdDest);
 
     // Restore user config after framework reinstallation
     updateSpinner.text = 'Restoring user configuration...';
@@ -330,21 +307,16 @@ export async function updateCommand(options) {
 
     logger.blank();
     logger.info('Updated files:');
-    if (updateTemplates) logger.dim('  ✓ .morph/templates/');
-    if (updateStandards) logger.dim('  ✓ .morph/standards/');
-    logger.dim('  ✓ .morph/config/agents.json');
-    logger.dim('  ✓ .morph/config/azure-pricing.json');
+    if (updateTemplates) logger.dim('  ✓ .morph/framework/templates/');
+    if (updateStandards) logger.dim('  ✓ .morph/framework/standards/');
+    logger.dim('  ✓ .morph/framework/agents.json');
     if (commandsCopied) logger.dim('  ✓ .claude/commands/');
 
-    if (symlinkCount > 0) {
-      const linkType = process.platform === 'win32' ? 'junction-linked' : 'symlinked';
-      logger.dim(`  ✓ .claude/skills/ (${symlinkCount} ${linkType})`);
-    } else if (copyCount > 0) {
-      logger.dim(`  ✓ .claude/skills/ (${copyCount} copied)`);
-      logger.warn(`  ⚠ Directory links not supported (copied instead). Skills won't auto-update.`);
-    }
-
-    logger.dim('  ✓ .claude/settings.local.json (agent-teams hooks)');
+    logger.dim(`  ✓ .claude/settings.local.json (${hooksResult.installed} hooks installed)`);
+    logger.dim('  ✓ .claude/skills/ (skills installed as directories)');
+    logger.dim('  ✓ .claude/agents/ (native subagents refreshed)');
+    logger.dim('  ✓ .claude/rules/ (path-scoped rules synced)');
+    logger.dim('  ✓ .claude/CLAUDE.md (runtime quick reference)');
     logger.dim('  ✓ CLAUDE.md');
     logger.blank();
     logger.info('Your config.json was preserved.');

package/src/commands/state/advance-phase.js

@@ -13,6 +13,7 @@ import chalk from 'chalk';
 import { loadState, saveState, getFeature, getApprovalGate } from '../../core/state/state-manager.js';
 import { PHASES, validatePhase } from './validate-phase.js';
 import { detectDesignSystem, hasUIAgentsActive } from '../../lib/detectors/design-system-detector.js';
+import { getOutputPath } from '../../core/paths/output-schema.js';
 import { shouldAutoApprove, autoCalculateTrust } from '../../lib/trust/trust-manager.js';
 import { validateSpec } from '../../lib/validators/spec-validator.js';
 import { validateTransition, getPhaseDisplayName } from '../../core/state/phase-state-machine.js';
@@ -401,7 +402,7 @@ function getPhaseGuidance(phase, feature) {
     ],
     'sync': [
       'Review decisions.md for standards to promote',
-      `Sync: morph-spec sync --path .morph/project/outputs/${feature}/decisions.md`
+      `Sync: morph-spec sync --path ${getOutputPath(feature, 'decisions')}`
     ]
   };
 
@@ -437,8 +438,8 @@ function designSystemGate(feature, projectPath = '.') {
       'Design system is required when UI agents (blazor-builder, ui-designer, css-specialist) are active',
       '',
       'Create a design system with one of these options:',
-      '  1. Project-level: .morph/project/design-system.md (shared across features)',
-      `  2. Feature-level: .morph/project/outputs/${feature}/ui-design-system.md (feature-specific)`,
+      '  1. Project-level: .morph/context/design-system.md (shared across features)',
+      `  2. Feature-level: ${getOutputPath(feature, 'uiDesignSystem')} (feature-specific)`,
       '  3. Auto-generate: morph-spec generate design-system (scans existing CSS)',
       '',
       'Or remove UI agents if they are not needed:',

package/src/commands/state/state.js

@@ -339,9 +339,16 @@ async function markOutputCommand(featureName, outputType, options) {
     logger.error('Missing required arguments');
     logger.dim('  Usage: morph-spec state mark-output <feature> <output-type>');
     logger.blank();
-    logger.dim('  Valid types: proposal, spec, contracts, tasks, decisions, recap');
-    logger.dim('               uiDesignSystem (or ui-design-system), uiMockups (or ui-mockups)');
-    logger.dim('               uiComponents (or ui-components), uiFlows (or ui-flows)');
+    logger.dim('  Valid types:');
+    logger.dim('    Standard: proposal, spec, contracts, tasks, decisions, recap');
+    logger.dim('    UI/UX:    uiDesignSystem, uiMockups, uiComponents, uiFlows');
+    logger.blank();
+    logger.dim('  Note: UI types also accept kebab-case (e.g., ui-design-system)');
+    logger.blank();
+    logger.dim('  Examples:');
+    logger.dim('    morph-spec state mark-output my-feature spec');
+    logger.dim('    morph-spec state mark-output my-feature uiDesignSystem');
+    logger.dim('    morph-spec state mark-output my-feature ui-design-system');
     process.exit(1);
   }
 

package/src/commands/state/validate-phase.js

@@ -71,11 +71,28 @@ const PHASES = {
   }
 };
 
+// Map output filenames to their phase subfolders
+const OUTPUT_PHASE_MAP = {
+  'proposal.md': '0-proposal',
+  'schema-analysis.md': '1-design',
+  'spec.md': '1-design',
+  'clarifications.md': '1-design',
+  'contracts.cs': '1-design',
+  'decisions.md': '1-design',
+  'ui-design-system.md': '2-ui',
+  'ui-mockups.md': '2-ui',
+  'ui-components.md': '2-ui',
+  'ui-flows.md': '2-ui',
+  'tasks.md': '3-tasks',
+  'recap.md': '4-implement'
+};
+
 /**
  * Check if output file exists
  */
 function checkOutput(featurePath, outputFile) {
-  const filePath = path.join(featurePath, outputFile);
+  const phaseDir = OUTPUT_PHASE_MAP[outputFile] || '';
+  const filePath = path.join(featurePath, phaseDir, outputFile);
   return fs.existsSync(filePath);
 }
 
@@ -83,7 +100,7 @@ function checkOutput(featurePath, outputFile) {
  * Validate phase requirements
  */
 function validatePhase(featureName, targetPhase) {
-  const featurePath = path.join(process.cwd(), '.morph/project/outputs', featureName);
+  const featurePath = path.join(process.cwd(), '.morph/features', featureName);
 
   // Check if feature directory exists
   if (!fs.existsSync(featurePath)) {

package/src/commands/templates/template-customize.js

@@ -9,7 +9,7 @@ import { logger } from '../../utils/logger.js';
 import { getTemplateById, resolveTemplatePathById } from '../../core/templates/template-registry.js';
 
 /**
- * Customize template command - copies framework template to project .morph/templates/
+ * Customize template command - copies framework template to project .morph/framework/templates/
  */
 export async function templateCustomizeCommand(templateId, options) {
   logger.header(`Customizing Template: ${templateId}`);
@@ -34,9 +34,9 @@ export async function templateCustomizeCommand(templateId, options) {
       process.exit(1);
     }
 
-    // 4. Destination is always project-local .morph/templates/
-    const destDir = join(projectPath, '.morph/templates', dirname(template.path));
-    const destPath = join(projectPath, '.morph/templates', template.path);
+    // 4. Destination is always project-local .morph/framework/templates/
+    const destDir = join(projectPath, '.morph/framework/templates', dirname(template.path));
+    const destPath = join(projectPath, '.morph/framework/templates', template.path);
 
     // 5. Check if already exists
     if (existsSync(destPath) && !options.force) {

package/src/commands/templates/template-render.js

@@ -111,7 +111,7 @@ export async function templateRenderCommand(templateId, outputPath, variablesJso
 
     if (!templatePath) {
       logger.error(`Template file not found for ${templateId}`);
-      logger.dim('  Searched in: .morph/templates/ and framework/templates/');
+      logger.dim('  Searched in: .morph/framework/templates/ and framework/templates/');
       process.exit(1);
     }
 

package/src/commands/templates/template-show.js

@@ -83,7 +83,7 @@ export async function templateShowCommand(templateId, options) {
         console.log(`  ${chalk.green(resolvedPath)}`);
         console.log(`  ${chalk.dim(`(${existsSync(resolvedPath) ? 'exists' : 'not found'})`)}`);
       } else {
-        console.log(`  ${chalk.red('Not found in .morph/templates/ or framework/templates/')}`);
+        console.log(`  ${chalk.red('Not found in .morph/framework/templates/ or framework/templates/')}`);
       }
       logger.blank();
     }