orbital-command 0.2.0 → 1.0.0

package/server/init.ts

@@ -1,11 +1,25 @@
 /**
- * Shared init logic — used by both the CLI (`orbital init`) and
- * programmatic callers (e.g. tests).
+ * Shared init logic — used by the wizard and
+ * programmatic callers (e.g. tests, API routes).
  */
 
 import fs from 'fs';
 import path from 'path';
 import { fileURLToPath } from 'url';
+import { GLOBAL_PRIMITIVES_DIR, ensureOrbitalHome } from './global-config.js';
+import {
+  saveManifest,
+  createManifest,
+  hashFile,
+  buildTemplateInventory,
+  templateFileRecord,
+  userFileRecord,
+  isSelfHosting,
+  getSymlinkTarget,
+} from './manifest.js';
+import type { OrbitalManifest } from './manifest-types.js';
+import { getTemplateChecksum } from './settings-sync.js';
+import { getPackageVersion as _getPackageVersionUtil } from './utils/package-info.js';
 
 const __filename = fileURLToPath(import.meta.url);
 const __dirname = path.dirname(__filename);
@@ -228,7 +242,8 @@ function generateManifest(config: Record<string, unknown>): string {
   lines.push('');
 
   lines.push('# ─── Entry point status ───');
-  lines.push(`WORKFLOW_ENTRY_STATUS="${(config.entryPoint as string) || (lists[0]?.id as string) || 'todo'}"`);
+  const entryPointId = (lists.find((l) => l.isEntryPoint)?.id as string) || (lists[0]?.id as string) || 'todo';
+  lines.push(`WORKFLOW_ENTRY_STATUS="${entryPointId}"`);
   lines.push('');
 
   const listMap = new Map(lists.map((l) => [l.id, l]));
@@ -255,6 +270,25 @@ function generateManifest(config: Record<string, unknown>): string {
   lines.push(')');
   lines.push('');
 
+  lines.push('# ─── Commit session branch patterns (regex) ───');
+  lines.push(`WORKFLOW_COMMIT_BRANCHES="${(config.commitBranchPatterns as string) ?? ''}"`);
+  lines.push('');
+
+  lines.push('# ─── Backward-compat direction aliases (alias:from:to:sessionKey) ───');
+  lines.push('WORKFLOW_DIRECTION_ALIASES=(');
+  for (const edge of (config.edges as Array<Record<string, unknown>>) || []) {
+    if (edge.direction !== 'forward' || !edge.dispatchOnly) continue;
+    const targetList = listMap.get(edge.to as string);
+    if (!targetList) continue;
+    const group = targetList.group as string | undefined;
+    if (group?.startsWith('deploy')) {
+      const sessionKey = (targetList.sessionKey as string) ?? '';
+      lines.push(`  "to-${edge.to as string}:${edge.from as string}:${edge.to as string}:${sessionKey}"`);
+    }
+  }
+  lines.push(')');
+  lines.push('');
+
   lines.push('# ─── Helper functions ──────────────────────────────');
   lines.push('');
   lines.push('status_to_dir() {');
@@ -489,20 +523,151 @@ function cleanEmptyDirs(dir: string): void {
   }
 }
 
+// ─── Manifest Building ──────────────────────────────────────
+
+/** Build a manifest by scanning .claude/ and classifying files against templates. */
+function buildInitManifest(
+  projectRoot: string,
+  claudeDir: string,
+  preset: string,
+): OrbitalManifest {
+  const selfHosting = isSelfHosting(projectRoot);
+  const templateInventory = buildTemplateInventory(TEMPLATES_DIR);
+  const pkg = getPackageVersion();
+
+  const manifest = createManifest(pkg, preset);
+
+  // Classify all template files
+  for (const [relPath, templateHash] of templateInventory) {
+    const absPath = path.join(claudeDir, relPath);
+
+    if (selfHosting) {
+      const symlinkTarget = getSymlinkTarget(claudeDir, relPath);
+      if (symlinkTarget) {
+        manifest.files[relPath] = templateFileRecord(templateHash, symlinkTarget);
+        continue;
+      }
+    }
+
+    if (fs.existsSync(absPath)) {
+      const fileHash = hashFile(absPath);
+      if (fileHash === templateHash) {
+        manifest.files[relPath] = templateFileRecord(templateHash);
+      } else {
+        // File exists but doesn't match template — classify as outdated
+        // (no prior install to compare against, so we can't know if user edited it)
+        manifest.files[relPath] = {
+          origin: 'template',
+          status: 'outdated',
+          templateHash,
+          installedHash: fileHash,
+        };
+      }
+    }
+    // File doesn't exist — it may not have been copied (e.g. skipped on non-force init)
+  }
+
+  // Scan managed directories for user-created files
+  for (const dir of ['hooks', 'skills', 'agents']) {
+    const dirPath = path.join(claudeDir, dir);
+    if (!fs.existsSync(dirPath)) continue;
+
+    walkDirForManifest(dirPath, dir, (relPath, absPath) => {
+      if (manifest.files[relPath]) return; // Already classified
+      const fileHash = hashFile(absPath);
+      manifest.files[relPath] = userFileRecord(fileHash);
+    });
+  }
+
+  // Record settings hooks checksum
+  const settingsHooksPath = path.join(TEMPLATES_DIR, 'settings-hooks.json');
+  if (fs.existsSync(settingsHooksPath)) {
+    manifest.settingsHooksChecksum = getTemplateChecksum(settingsHooksPath);
+  }
+
+  // Record gitignore entries
+  manifest.gitignoreEntries = [
+    'scopes/',
+    '.claude/orbital/',
+    '.claude/orbital-events/',
+    '.claude/config/workflow-manifest.sh',
+  ];
+
+  return manifest;
+}
+
+function getPackageVersion(): string {
+  return _getPackageVersionUtil(PACKAGE_ROOT);
+}
+
+/** Recursively walk a directory for manifest building. */
+function walkDirForManifest(
+  dirPath: string,
+  prefix: string,
+  fn: (relPath: string, absPath: string) => void,
+): void {
+  if (!fs.existsSync(dirPath)) return;
+  for (const entry of fs.readdirSync(dirPath, { withFileTypes: true })) {
+    if (entry.name.startsWith('.')) continue;
+    const absPath = path.join(dirPath, entry.name);
+    const relPath = `${prefix}/${entry.name}`;
+    // Follow symlinks: use stat() to check if target is a directory
+    const stat = fs.statSync(absPath);
+    if (stat.isDirectory()) {
+      walkDirForManifest(absPath, relPath, fn);
+    } else {
+      fn(relPath, absPath);
+    }
+  }
+}
+
 // ─── Exports ─────────────────────────────────────────────────
 
-export { TEMPLATES_DIR, ensureDir };
+/** Seed ~/.orbital/primitives/ from package templates. Called by init, update, and server startup. */
+export function seedGlobalPrimitives(): void {
+  ensureOrbitalHome();
+  for (const type of ['hooks', 'skills', 'agents'] as const) {
+    const src = path.join(TEMPLATES_DIR, type);
+    const dest = path.join(GLOBAL_PRIMITIVES_DIR, type);
+    if (fs.existsSync(src)) {
+      copyDirSync(src, dest, { overwrite: true });
+    }
+  }
+}
+
+export { TEMPLATES_DIR, ensureDir, cleanEmptyDirs, chmodScripts, listTemplateFiles, writeManifest, generateIndexMd, getPackageVersion };
+
+// Re-export manifest utilities for CLI access via loadSharedModule()
+export { loadManifest, saveManifest, hashFile, buildTemplateInventory, refreshFileStatuses, summarizeManifest } from './manifest.js';
+export { validate, formatValidationReport } from './validator.js';
+
+// Re-export update and uninstall from their new homes (backward compat for loadSharedModule)
+export { runUpdate, type UpdateOptions } from './update.js';
+export { runUninstall, type UninstallOptions } from './uninstall.js';
 
 export interface InitOptions {
   force?: boolean;
+  quiet?: boolean;              // suppress console output (used by wizard)
+  preset?: string;              // workflow preset name (default: 'default')
+  projectName?: string;         // override auto-detected project name
+  serverPort?: number;          // override default server port
+  clientPort?: number;          // override default client port
+  commands?: Partial<Record<string, string | null>>; // override detected commands
 }
 
 export function runInit(projectRoot: string, options: InitOptions = {}): void {
   const force = options.force ?? false;
+  const quiet = options.quiet ?? false;
+  const selectedPreset = options.preset || 'default';
   const claudeDir = path.join(projectRoot, '.claude');
 
-  console.log(`\nOrbital Command — init`);
-  console.log(`Project root: ${projectRoot}\n`);
+  // eslint-disable-next-line @typescript-eslint/no-empty-function
+  const log = quiet ? (..._args: unknown[]) => {} : console.log.bind(console);
+  // eslint-disable-next-line @typescript-eslint/no-empty-function
+  const warn = quiet ? (..._args: unknown[]) => {} : console.warn.bind(console);
+
+  log(`\nOrbital Command — init`);
+  log(`Project root: ${projectRoot}\n`);
 
   // 1. Create directories
   const dirs = [
@@ -513,24 +678,26 @@ export function runInit(projectRoot: string, options: InitOptions = {}): void {
   ];
   for (const dir of dirs) {
     const wasCreated = ensureDir(dir);
-    console.log(`  ${wasCreated ? 'Created' : 'Exists '}  ${path.relative(projectRoot, dir)}/`);
+    log(`  ${wasCreated ? 'Created' : 'Exists '}  ${path.relative(projectRoot, dir)}/`);
   }
 
-  // 1b. Create scopes/ subdirectories from the default workflow preset
+  // 1b. Create scopes/ subdirectories from the selected workflow preset
+  const selectedPresetPath = path.join(TEMPLATES_DIR, 'presets', `${selectedPreset}.json`);
   const defaultPresetPath = path.join(TEMPLATES_DIR, 'presets', 'default.json');
+  const presetPath = fs.existsSync(selectedPresetPath) ? selectedPresetPath : defaultPresetPath;
   let scopeDirs = ['icebox'];
   try {
-    const preset = JSON.parse(fs.readFileSync(defaultPresetPath, 'utf8'));
+    const preset = JSON.parse(fs.readFileSync(presetPath, 'utf8'));
     if (preset.lists && Array.isArray(preset.lists)) {
       scopeDirs = preset.lists.filter((l: Record<string, unknown>) => l.hasDirectory).map((l: Record<string, unknown>) => l.id as string);
     }
   } catch {
-    console.warn('  Warning: could not load default preset, creating scopes/icebox/ only');
+    warn('  Warning: could not load preset, creating scopes/icebox/ only');
   }
   for (const dirId of scopeDirs) {
     const scopeDir = path.join(projectRoot, 'scopes', dirId);
     const wasCreated = ensureDir(scopeDir);
-    console.log(`  ${wasCreated ? 'Created' : 'Exists '}  scopes/${dirId}/`);
+    log(`  ${wasCreated ? 'Created' : 'Exists '}  scopes/${dirId}/`);
   }
 
   // 1c. Copy scope template
@@ -539,9 +706,9 @@ export function runInit(projectRoot: string, options: InitOptions = {}): void {
   if (fs.existsSync(scopeTemplateSrc)) {
     if (force || !fs.existsSync(scopeTemplateDest)) {
       fs.copyFileSync(scopeTemplateSrc, scopeTemplateDest);
-      console.log(`  ${force ? 'Reset  ' : 'Created'}  scopes/_template.md`);
+      log(`  ${force ? 'Reset  ' : 'Created'}  scopes/_template.md`);
     } else {
-      console.log(`  Exists   scopes/_template.md`);
+      log(`  Exists   scopes/_template.md`);
     }
   }
 
@@ -552,75 +719,97 @@ export function runInit(projectRoot: string, options: InitOptions = {}): void {
   if (configIsNew) {
     if (fs.existsSync(configSrc)) {
       fs.copyFileSync(configSrc, configDest);
-      console.log(`  Created  .claude/orbital.config.json`);
+      // Apply wizard-collected or auto-detected values
+      try {
+        const config = JSON.parse(fs.readFileSync(configDest, 'utf8'));
+        config.projectName = options.projectName || path.basename(projectRoot)
+          .replace(/[-_]+/g, ' ')
+          .replace(/\b\w/g, c => c.toUpperCase());
+        if (options.serverPort) config.serverPort = options.serverPort;
+        if (options.clientPort) config.clientPort = options.clientPort;
+        fs.writeFileSync(configDest, JSON.stringify(config, null, 2) + '\n', 'utf8');
+      } catch { /* leave template default */ }
+      log(`  Created  .claude/orbital.config.json`);
     } else {
       const defaultConfig = {
-        serverPort: 4444,
-        clientPort: 4445,
-        projectName: path.basename(projectRoot),
+        serverPort: options.serverPort || 4444,
+        clientPort: options.clientPort || 4445,
+        projectName: options.projectName || path.basename(projectRoot),
       };
       fs.writeFileSync(configDest, JSON.stringify(defaultConfig, null, 2) + '\n', 'utf8');
-      console.log(`  Created  .claude/orbital.config.json (default)`);
+      log(`  Created  .claude/orbital.config.json (default)`);
     }
 
-    // Auto-detect project commands from package.json
-    const pkgJsonPath = path.join(projectRoot, 'package.json');
-    if (fs.existsSync(pkgJsonPath)) {
+    // Apply wizard-provided commands or auto-detect from package.json
+    if (options.commands) {
       try {
-        const pkg = JSON.parse(fs.readFileSync(pkgJsonPath, 'utf8'));
-        const scripts = pkg.scripts || {};
         const config = JSON.parse(fs.readFileSync(configDest, 'utf8'));
         if (!config.commands) config.commands = {};
-        let detected = 0;
-
-        if (scripts.typecheck || scripts['type-check']) {
-          config.commands.typeCheck = `npm run ${scripts.typecheck ? 'typecheck' : 'type-check'}`;
-          detected++;
-        }
-        if (scripts.lint) { config.commands.lint = 'npm run lint'; detected++; }
-        if (scripts.build) { config.commands.build = 'npm run build'; detected++; }
-        if (scripts.test) { config.commands.test = 'npm run test'; detected++; }
-
-        if (detected > 0) {
-          fs.writeFileSync(configDest, JSON.stringify(config, null, 2) + '\n', 'utf8');
-          console.log(`  Detected ${detected} project command(s) from package.json`);
-        }
+        Object.assign(config.commands, options.commands);
+        const commandCount = Object.values(options.commands).filter(v => v !== null).length;
+        fs.writeFileSync(configDest, JSON.stringify(config, null, 2) + '\n', 'utf8');
+        if (commandCount > 0) log(`  Applied  ${commandCount} project command(s)`);
       } catch { /* leave defaults */ }
+    } else {
+      // Auto-detect project commands from package.json
+      const pkgJsonPath = path.join(projectRoot, 'package.json');
+      if (fs.existsSync(pkgJsonPath)) {
+        try {
+          const pkg = JSON.parse(fs.readFileSync(pkgJsonPath, 'utf8'));
+          const scripts = pkg.scripts || {};
+          const config = JSON.parse(fs.readFileSync(configDest, 'utf8'));
+          if (!config.commands) config.commands = {};
+          let detected = 0;
+
+          if (scripts.typecheck || scripts['type-check']) {
+            config.commands.typeCheck = `npm run ${scripts.typecheck ? 'typecheck' : 'type-check'}`;
+            detected++;
+          }
+          if (scripts.lint) { config.commands.lint = 'npm run lint'; detected++; }
+          if (scripts.build) { config.commands.build = 'npm run build'; detected++; }
+          if (scripts.test) { config.commands.test = 'npm run test'; detected++; }
+
+          if (detected > 0) {
+            fs.writeFileSync(configDest, JSON.stringify(config, null, 2) + '\n', 'utf8');
+            log(`  Detected ${detected} project command(s) from package.json`);
+          }
+        } catch { /* leave defaults */ }
+      }
     }
   } else {
-    console.log(`  Exists   .claude/orbital.config.json`);
+    log(`  Exists   .claude/orbital.config.json`);
   }
 
   // 3. Copy hooks
-  console.log('');
+  log('');
   const hooksSrc = path.join(TEMPLATES_DIR, 'hooks');
   const hooksDest = path.join(claudeDir, 'hooks');
   if (force) {
     const pruned = pruneStaleEntries(hooksSrc, hooksDest);
-    if (pruned > 0) console.log(`  Pruned   ${pruned} stale hook entries`);
+    if (pruned > 0) log(`  Pruned   ${pruned} stale hook entries`);
   }
   const hooksResult = copyDirSync(hooksSrc, hooksDest, { overwrite: force });
-  console.log(`  Hooks    ${hooksResult.created.length} copied, ${hooksResult.skipped.length} skipped`);
+  log(`  Hooks    ${hooksResult.created.length} copied, ${hooksResult.skipped.length} skipped`);
 
   // 4. Copy skills
   const skillsSrc = path.join(TEMPLATES_DIR, 'skills');
   const skillsDest = path.join(claudeDir, 'skills');
   if (force) {
     const pruned = pruneStaleEntries(skillsSrc, skillsDest);
-    if (pruned > 0) console.log(`  Pruned   ${pruned} stale skill entries`);
+    if (pruned > 0) log(`  Pruned   ${pruned} stale skill entries`);
   }
   const skillsResult = copyDirSync(skillsSrc, skillsDest, { overwrite: force });
-  console.log(`  Skills   ${skillsResult.created.length} copied, ${skillsResult.skipped.length} skipped`);
+  log(`  Skills   ${skillsResult.created.length} copied, ${skillsResult.skipped.length} skipped`);
 
   // 5. Copy agents
   const agentsSrc = path.join(TEMPLATES_DIR, 'agents');
   const agentsDest = path.join(claudeDir, 'agents');
   if (force) {
     const pruned = pruneStaleEntries(agentsSrc, agentsDest);
-    if (pruned > 0) console.log(`  Pruned   ${pruned} stale agent entries`);
+    if (pruned > 0) log(`  Pruned   ${pruned} stale agent entries`);
   }
   const agentsResult = copyDirSync(agentsSrc, agentsDest, { overwrite: force });
-  console.log(`  Agents   ${agentsResult.created.length} copied, ${agentsResult.skipped.length} skipped`);
+  log(`  Agents   ${agentsResult.created.length} copied, ${agentsResult.skipped.length} skipped`);
 
   // 6. Copy workflow presets
   const presetsSrc = path.join(TEMPLATES_DIR, 'presets');
@@ -628,22 +817,22 @@ export function runInit(projectRoot: string, options: InitOptions = {}): void {
   if (fs.existsSync(presetsSrc) && fs.readdirSync(presetsSrc).length > 0) {
     if (force) {
       const pruned = pruneStaleEntries(presetsSrc, presetsDest);
-      if (pruned > 0) console.log(`  Pruned   ${pruned} stale preset entries`);
+      if (pruned > 0) log(`  Pruned   ${pruned} stale preset entries`);
     }
     const presetsResult = copyDirSync(presetsSrc, presetsDest, { overwrite: force });
-    console.log(`  Presets  ${presetsResult.created.length} copied, ${presetsResult.skipped.length} skipped`);
+    log(`  Presets  ${presetsResult.created.length} copied, ${presetsResult.skipped.length} skipped`);
   }
 
   // 6b. Reset active workflow config when --force, or create if missing
   const activeWorkflowDest = path.join(claudeDir, 'config', 'workflow.json');
   if (force) {
-    fs.copyFileSync(defaultPresetPath, activeWorkflowDest);
-    console.log(`  Reset    .claude/config/workflow.json (default workflow)`);
+    fs.copyFileSync(presetPath, activeWorkflowDest);
+    log(`  Reset    .claude/config/workflow.json (${selectedPreset} workflow)`);
   } else if (!fs.existsSync(activeWorkflowDest)) {
-    fs.copyFileSync(defaultPresetPath, activeWorkflowDest);
-    console.log(`  Created  .claude/config/workflow.json`);
+    fs.copyFileSync(presetPath, activeWorkflowDest);
+    log(`  Created  .claude/config/workflow.json (${selectedPreset})`);
   } else {
-    console.log(`  Exists   .claude/config/workflow.json`);
+    log(`  Exists   .claude/config/workflow.json`);
   }
 
   // 7. Copy agent-triggers.json
@@ -652,9 +841,9 @@ export function runInit(projectRoot: string, options: InitOptions = {}): void {
   if (fs.existsSync(triggersSrc)) {
     if (force || !fs.existsSync(triggersDest)) {
       fs.copyFileSync(triggersSrc, triggersDest);
-      console.log(`  Created  .claude/config/agent-triggers.json`);
+      log(`  Created  .claude/config/agent-triggers.json`);
     } else {
-      console.log(`  Exists   .claude/config/agent-triggers.json`);
+      log(`  Exists   .claude/config/agent-triggers.json`);
     }
   }
 
@@ -663,7 +852,7 @@ export function runInit(projectRoot: string, options: InitOptions = {}): void {
   const quickDest = path.join(claudeDir, 'quick');
   if (fs.existsSync(quickSrc)) {
     const quickResult = copyDirSync(quickSrc, quickDest, { overwrite: force });
-    console.log(`  Quick    ${quickResult.created.length} copied, ${quickResult.skipped.length} skipped`);
+    log(`  Quick    ${quickResult.created.length} copied, ${quickResult.skipped.length} skipped`);
   }
 
   // 7c. Copy anti-patterns/ templates
@@ -671,7 +860,7 @@ export function runInit(projectRoot: string, options: InitOptions = {}): void {
   const antiDest = path.join(claudeDir, 'anti-patterns');
   if (fs.existsSync(antiSrc)) {
     const antiResult = copyDirSync(antiSrc, antiDest, { overwrite: force });
-    console.log(`  Anti-pat ${antiResult.created.length} copied, ${antiResult.skipped.length} skipped`);
+    log(`  Anti-pat ${antiResult.created.length} copied, ${antiResult.skipped.length} skipped`);
   }
 
   // 7d. Copy lessons-learned.md
@@ -680,212 +869,55 @@ export function runInit(projectRoot: string, options: InitOptions = {}): void {
   if (fs.existsSync(lessonsSrc)) {
     if (force || !fs.existsSync(lessonsDest)) {
       fs.copyFileSync(lessonsSrc, lessonsDest);
-      console.log(`  Created  .claude/lessons-learned.md`);
+      log(`  Created  .claude/lessons-learned.md`);
     } else {
-      console.log(`  Exists   .claude/lessons-learned.md`);
+      log(`  Exists   .claude/lessons-learned.md`);
     }
   }
 
   // 7e. Generate workflow manifest
   const manifestOk = writeManifest(claudeDir);
-  console.log(`  ${manifestOk ? 'Created' : 'Skipped'}  .claude/config/workflow-manifest.sh`);
+  log(`  ${manifestOk ? 'Created' : 'Skipped'}  .claude/config/workflow-manifest.sh`);
 
   // 7f. Generate INDEX.md
   const indexDest = path.join(claudeDir, 'INDEX.md');
   if (force || !fs.existsSync(indexDest)) {
     const indexContent = generateIndexMd(projectRoot, claudeDir);
     fs.writeFileSync(indexDest, indexContent, 'utf8');
-    console.log(`  ${force ? 'Reset  ' : 'Created'}  .claude/INDEX.md`);
+    log(`  ${force ? 'Reset  ' : 'Created'}  .claude/INDEX.md`);
   } else {
-    console.log(`  Exists   .claude/INDEX.md`);
+    log(`  Exists   .claude/INDEX.md`);
   }
 
   // 8. Merge hook registrations into settings.local.json
-  console.log('');
+  log('');
   const settingsTarget = path.join(claudeDir, 'settings.local.json');
   const settingsSrc = path.join(TEMPLATES_DIR, 'settings-hooks.json');
   mergeSettingsHooks(settingsTarget, settingsSrc);
-  console.log(`  Merged   hook registrations into .claude/settings.local.json`);
+  log(`  Merged   hook registrations into .claude/settings.local.json`);
 
   // 9. Update .gitignore
   const gitignoreUpdated = updateGitignore(projectRoot);
-  console.log(`  ${gitignoreUpdated ? 'Updated' : 'Exists '}  .gitignore (Orbital patterns)`);
+  log(`  ${gitignoreUpdated ? 'Updated' : 'Exists '}  .gitignore (Orbital patterns)`);
 
   // 10. Make hook scripts executable
   chmodScripts(hooksDest);
-  console.log(`  chmod    hook scripts set to executable`);
+  log(`  chmod    hook scripts set to executable`);
+
+  // 11. Seed global primitives from package templates
+  seedGlobalPrimitives();
+  log(`  Seeded   global primitives (~/.orbital/primitives/)`);
+
+  // 12. Build and save manifest
+  const manifest = buildInitManifest(projectRoot, claudeDir, selectedPreset);
+  saveManifest(projectRoot, manifest);
+  log(`  Created  .claude/orbital-manifest.json (${Object.keys(manifest.files).length} files tracked)`);
 
   // Summary
   const totalCreated = hooksResult.created.length + skillsResult.created.length + agentsResult.created.length;
   const totalSkipped = hooksResult.skipped.length + skillsResult.skipped.length + agentsResult.skipped.length;
-  console.log(`\nDone. ${totalCreated} files installed, ${totalSkipped} skipped (use --force to overwrite).`);
-}
-
-export function runUpdate(projectRoot: string): void {
-  const claudeDir = path.join(projectRoot, '.claude');
-
-  console.log(`\nOrbital Command — update`);
-  console.log(`Project root: ${projectRoot}\n`);
-
-  // 1. Copy hooks (overwrite) — prune stale entries first
-  const hooksSrc = path.join(TEMPLATES_DIR, 'hooks');
-  const hooksDest = path.join(claudeDir, 'hooks');
-  const hooksPruned = pruneStaleEntries(hooksSrc, hooksDest);
-  if (hooksPruned > 0) console.log(`  Pruned   ${hooksPruned} stale hook entries`);
-  const hooksResult = copyDirSync(hooksSrc, hooksDest, { overwrite: true });
-  console.log(`  Hooks    ${hooksResult.created.length} updated`);
-
-  // 2. Copy skills (overwrite) — prune stale entries first
-  const skillsSrc = path.join(TEMPLATES_DIR, 'skills');
-  const skillsDest = path.join(claudeDir, 'skills');
-  const skillsPruned = pruneStaleEntries(skillsSrc, skillsDest);
-  if (skillsPruned > 0) console.log(`  Pruned   ${skillsPruned} stale skill entries`);
-  const skillsResult = copyDirSync(skillsSrc, skillsDest, { overwrite: true });
-  console.log(`  Skills   ${skillsResult.created.length} updated`);
-
-  // 3. Copy agents (overwrite) — prune stale entries first
-  const agentsSrc = path.join(TEMPLATES_DIR, 'agents');
-  const agentsDest = path.join(claudeDir, 'agents');
-  const agentsPruned = pruneStaleEntries(agentsSrc, agentsDest);
-  if (agentsPruned > 0) console.log(`  Pruned   ${agentsPruned} stale agent entries`);
-  const agentsResult = copyDirSync(agentsSrc, agentsDest, { overwrite: true });
-  console.log(`  Agents   ${agentsResult.created.length} updated`);
-
-  // 4. Update workflow presets — prune stale entries first
-  const presetsSrc = path.join(TEMPLATES_DIR, 'presets');
-  const presetsDest = path.join(claudeDir, 'config', 'workflows');
-  if (fs.existsSync(presetsSrc) && fs.readdirSync(presetsSrc).length > 0) {
-    const presetsPruned = pruneStaleEntries(presetsSrc, presetsDest);
-    if (presetsPruned > 0) console.log(`  Pruned   ${presetsPruned} stale preset entries`);
-    const presetsResult = copyDirSync(presetsSrc, presetsDest, { overwrite: true });
-    console.log(`  Presets  ${presetsResult.created.length} updated`);
-  }
-
-  // 5. Update quick/, anti-patterns/, lessons-learned, scope template
-  const quickSrc = path.join(TEMPLATES_DIR, 'quick');
-  const quickDest = path.join(claudeDir, 'quick');
-  if (fs.existsSync(quickSrc)) {
-    const quickResult = copyDirSync(quickSrc, quickDest, { overwrite: true });
-    console.log(`  Quick    ${quickResult.created.length} updated`);
-  }
-
-  const antiSrc = path.join(TEMPLATES_DIR, 'anti-patterns');
-  const antiDest = path.join(claudeDir, 'anti-patterns');
-  if (fs.existsSync(antiSrc)) {
-    const antiResult = copyDirSync(antiSrc, antiDest, { overwrite: true });
-    console.log(`  Anti-pat ${antiResult.created.length} updated`);
-  }
-
-  const lessonsSrc = path.join(TEMPLATES_DIR, 'lessons-learned.md');
-  const lessonsDest = path.join(claudeDir, 'lessons-learned.md');
-  if (fs.existsSync(lessonsSrc) && !fs.existsSync(lessonsDest)) {
-    fs.copyFileSync(lessonsSrc, lessonsDest);
-    console.log(`  Created  .claude/lessons-learned.md`);
-  }
-
-  const scopeTemplateSrc = path.join(TEMPLATES_DIR, 'scopes', '_template.md');
-  const scopeTemplateDest = path.join(projectRoot, 'scopes', '_template.md');
-  if (fs.existsSync(scopeTemplateSrc)) {
-    ensureDir(path.join(projectRoot, 'scopes'));
-    fs.copyFileSync(scopeTemplateSrc, scopeTemplateDest);
-    console.log(`  Updated  scopes/_template.md`);
-  }
-
-  // 5b. Regenerate workflow manifest
-  const manifestOk = writeManifest(claudeDir);
-  console.log(`  ${manifestOk ? 'Updated' : 'Skipped'}  .claude/config/workflow-manifest.sh`);
-
-  // 6. Re-merge settings hooks
-  const settingsTarget = path.join(claudeDir, 'settings.local.json');
-  const settingsSrc = path.join(TEMPLATES_DIR, 'settings-hooks.json');
-  mergeSettingsHooks(settingsTarget, settingsSrc);
-  console.log(`  Merged   hook registrations into .claude/settings.local.json`);
-
-  // 7. Make hook scripts executable
-  chmodScripts(hooksDest);
-  console.log(`  chmod    hook scripts set to executable`);
-
-  console.log(`\nUpdate complete.\n`);
+  log(`\nDone. ${totalCreated} files installed, ${totalSkipped} skipped (use --force to overwrite).`);
 }
 
-export function runUninstall(projectRoot: string): void {
-  const claudeDir = path.join(projectRoot, '.claude');
-
-  console.log(`\nOrbital Command — uninstall`);
-  console.log(`Project root: ${projectRoot}\n`);
-
-  let removedCount = 0;
-
-  // 1. Remove orbital hooks from settings.local.json
-  const settingsPath = path.join(claudeDir, 'settings.local.json');
-  if (fs.existsSync(settingsPath)) {
-    try {
-      const settings = JSON.parse(fs.readFileSync(settingsPath, 'utf8'));
-      if (settings.hooks) {
-        for (const [event] of Object.entries(settings.hooks)) {
-          for (const group of settings.hooks[event]) {
-            if (group.hooks) {
-              const before = group.hooks.length;
-              group.hooks = group.hooks.filter((h: HookEntry) => !h._orbital);
-              removedCount += before - group.hooks.length;
-            }
-          }
-          settings.hooks[event] = settings.hooks[event].filter(
-            (g: HookGroup) => g.hooks && g.hooks.length > 0
-          );
-          if (settings.hooks[event].length === 0) {
-            delete settings.hooks[event];
-          }
-        }
-        if (Object.keys(settings.hooks).length === 0) {
-          delete settings.hooks;
-        }
-        fs.writeFileSync(settingsPath, JSON.stringify(settings, null, 2) + '\n', 'utf8');
-        console.log(`  Removed  ${removedCount} orbital hook registrations from settings.local.json`);
-      }
-    } catch {
-      console.warn('  Warning: could not parse settings.local.json');
-    }
-  }
-
-  // 2. Delete hooks that came from templates
-  const hookFiles = listTemplateFiles(path.join(TEMPLATES_DIR, 'hooks'), path.join(claudeDir, 'hooks'));
-  let hooksRemoved = 0;
-  for (const f of hookFiles) {
-    if (fs.existsSync(f)) {
-      fs.unlinkSync(f);
-      hooksRemoved++;
-    }
-  }
-  console.log(`  Removed  ${hooksRemoved} hook scripts`);
-
-  // 3. Delete skills that came from templates
-  const skillFiles = listTemplateFiles(path.join(TEMPLATES_DIR, 'skills'), path.join(claudeDir, 'skills'));
-  let skillsRemoved = 0;
-  for (const f of skillFiles) {
-    if (fs.existsSync(f)) {
-      fs.unlinkSync(f);
-      skillsRemoved++;
-    }
-  }
-  const skillsDest = path.join(claudeDir, 'skills');
-  if (fs.existsSync(skillsDest)) cleanEmptyDirs(skillsDest);
-  console.log(`  Removed  ${skillsRemoved} skill files`);
-
-  // 4. Delete agents that came from templates
-  const agentFiles = listTemplateFiles(path.join(TEMPLATES_DIR, 'agents'), path.join(claudeDir, 'agents'));
-  let agentsRemoved = 0;
-  for (const f of agentFiles) {
-    if (fs.existsSync(f)) {
-      fs.unlinkSync(f);
-      agentsRemoved++;
-    }
-  }
-  const agentsDest = path.join(claudeDir, 'agents');
-  if (fs.existsSync(agentsDest)) cleanEmptyDirs(agentsDest);
-  console.log(`  Removed  ${agentsRemoved} agent files`);
-
-  const total = removedCount + hooksRemoved + skillsRemoved + agentsRemoved;
-  console.log(`\nUninstall complete. ${total} items removed.`);
-  console.log(`Note: scopes/ and .claude/orbital-events/ were preserved.\n`);
-}
+// runUpdate and runUninstall have been extracted to update.ts and uninstall.ts
+// and are re-exported above for backward compatibility.