🐛 fix(core): prevent overwriting user customizations on re-install and update

- **`copyRecursive`**: only copies files if destination does not exist, preserving user modifications
- **`global update`**: uses `quiet: true` (merge strategy) instead of `force: true` (overwrite strategy), preventing agent replacement with template defaults
- **`init` command**: adds `--yes` flag for safe auto-confirm merge (does not overwrite), separate from destructive `--force`
- Bump version to 1.3.9 and update migration manifest, CHANGELOG, and docs

Author: defuj

CHANGELOG.md

@@ -91,6 +91,34 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - `.opencode/skills/global-install/SKILL.md`: documented all 4 path rewrite locations with table
 - `package.json`: version bumped to 1.3.8
 
+### Fixed
+
+- **`copyRecursive` no longer overwrites existing files** — `copyFileSync` is now gated by `!existsSync(destPath)`. Previously every file in directories (skills/, prompts/, commands/, etc.) was overwritten on re-install, destroying any user modifications.
+- **`global update` no longer uses `--force`** — changed from `force: true` to `quiet: true`. Previously `global update` passed `force: true` which triggered `source-wins` strategy, overwriting all user-customized agents with template defaults. Now it uses merge strategy (preserves user changes).
+- **New `--yes` flag** — added `--yes` to `init` command for auto-confirm merge without overwriting. Semantics: `--yes` skips the confirmation prompt but still uses merge strategy. `--force` skips prompt AND overwrites with template (destructive).
+
+### Changed
+
+- `bin/commands/init.mjs`: `installGlobal()` prompt now checks `options.quiet` (auto-confirm) separately from `options.force` (overwrite). `copyRecursive()` only copies non-existing files. `init()` maps `--yes` → `options.quiet`.
+  |- `bin/commands/global-cmd.mjs`: `cmdUpdate()` passes `quiet: true` instead of `force: true` to `init()`.
+  |- `bin/init.mjs`: added `--yes` option to `init` command.
+
+## [1.3.9] - 2026-06-27
+
+### Fixed
+
+- **User config preservation on re-install** — three issues that caused user modifications to `opencode.jsonc` and global files to be lost:
+  - `copyRecursive()` no longer overwrites existing files (only copies new ones)
+  - `global update` uses `quiet: true` (merge) instead of `force: true` (overwrite)
+  - New `--yes` flag for safe auto-confirm merge (separate from destructive `--force`)
+
+### Changed
+
+- `bin/commands/init.mjs`: `copyRecursive()` gated by `!existsSync(destPath)`; `installGlobal()` uses `options.quiet` for prompt skip; `init()` maps `--yes` → `quiet`
+- `bin/commands/global-cmd.mjs`: `cmdUpdate()` passes `quiet: true` instead of `force: true`
+- `bin/init.mjs`: added `--yes` option to `init` command
+- `package.json`: version bumped to 1.3.9
+
 ## [1.3.4] - 2026-06-25
 
 ### Added

bin/commands/global-cmd.mjs

@@ -153,10 +153,10 @@ async function cmdUpdate() {
 
   console.log(`  Current: v${currentVersion} → Latest: v${latestVersion}`);
 
-  // Re-run the global install (re-copy template)
+  // Re-run the global install (re-copy template, merge not overwrite)
   info('Updating global install...');
   const { init } = await import('./init.mjs');
-  await init({ global: true, force: true, skipInstall: false, dir: process.cwd() });
+  await init({ global: true, quiet: true, skipInstall: false, dir: process.cwd() });
 
   success(`Global install updated to v${latestVersion}`);
 }

bin/commands/init.mjs

@@ -56,7 +56,8 @@ function copyRecursive(src, dest) {
     const destPath = join(dest, entry.name);
     if (entry.isDirectory()) {
       copyRecursive(srcPath, destPath);
-    } else {
+    } else if (!existsSync(destPath)) {
+      // Only copy if destination does NOT exist — preserves user modifications
       copyFileSync(srcPath, destPath);
     }
   }
@@ -246,7 +247,7 @@ async function installGlobal(options) {
   // 2. Check if already installed
   const jsoncPath = join(opencodeHome, 'opencode.jsonc');
   const jsonPath = join(opencodeHome, 'opencode.json');
-  if ((existsSync(jsoncPath) || existsSync(jsonPath)) && !options.force) {
+  if ((existsSync(jsoncPath) || existsSync(jsonPath)) && !options.quiet && !options.force) {
     warn(`OpenCode config already exists at ${opencodeHome}`);
     const rl = await import('readline/promises');
     const readline = rl.createInterface({ input: process.stdin, output: process.stdout });
@@ -643,6 +644,9 @@ async function initLocal(options) {
  *   default   →  check global, then choose initLocal() (per-project)
  */
 export async function init(options) {
+  // Map --yes to quiet (auto-confirm merge without overwriting)
+  if (options.yes) options.quiet = true;
+
   if (options.global) return installGlobal(options);
   if (options.local) return initLocal(options);
 

bin/init.mjs

@@ -34,6 +34,7 @@ program
   .option('--skip-install', 'Skip npm/bun install step in .opencode/')
   .option('--global', 'Install globally instead of per-project')
   .option('--local', 'Force local copy even when global install exists')
+  .option('--yes', 'Auto-confirm merge without overwriting')
   .action(init);
 
 program

bin/migrations/001_initial_setup.mjs

@@ -1,6 +1,6 @@
 /**
  * Migration 001: Initial Setup
- * Version: 1.3.8
+ * Version: 1.3.9
  *
  * Establishes the migration system foundation:
  * - Ensures .kit-version file exists in target .opencode/
@@ -20,7 +20,7 @@
  * @param {object} opts.path - Node path module
  */
 export default {
-  version: '1.3.8',
+  version: '1.3.9',
   description:
     'Initialize migration system — establish .kit-version tracking and validate config structure',
 
@@ -36,7 +36,7 @@ export default {
     // Ensure .kit-version file exists
     const versionFile = path.join(opencodeDir, '.kit-version');
     if (!fs.existsSync(versionFile)) {
-      fs.writeFileSync(versionFile, '1.3.8\n', 'utf-8');
+      fs.writeFileSync(versionFile, '1.3.9\n', 'utf-8');
     }
 
     // Validate config has agent and permission fields

bin/migrations/manifest.json

@@ -1,6 +1,6 @@
 {
   "001_initial_setup.mjs": {
-    "version": "1.3.8",
+    "version": "1.3.9",
     "description": "Initialize migration system — establish .kit-version tracking and validate config structure"
   }
 }

index.html

@@ -2954,7 +2954,7 @@ <h2>One command, <span class="text-primary">any way you
                     ready</span></div>
                 <div class="code-line code-output code-highlight"><span
                     style="color: var(--success)"> ✅</span> <span
-                    style="color: var(--text-primary)">opencode-agent-kit v1.3.8
+                    style="color: var(--text-primary)">opencode-agent-kit v1.3.9
                     installed globally!</span></div>
               </div>
             </div>
@@ -3360,7 +3360,7 @@ <h5 class="footer-col-title">Resources</h5>
               delay: 3200,
             },
             {
-              text: '<span style="color: var(--success)">  ✅</span> <span style="color: var(--text-primary)">opencode-agent-kit v1.3.8 installed globally</span>',
+              text: '<span style="color: var(--success)">  ✅</span> <span style="color: var(--text-primary)">opencode-agent-kit v1.3.9 installed globally</span>',
               delay: 4000,
             },
           ];
@@ -3401,7 +3401,7 @@ <h5 class="footer-col-title">Resources</h5>
           } else {
             // Show final state for reduced motion
             termBody.innerHTML =
-              '<span class="terminal-preview-prompt">$</span> npx opencode-agent-kit init --global<br><span style="color: var(--success)">  ✅</span> <span style="color: var(--text-primary)">opencode-agent-kit v1.3.8 installed globally</span>';
+              '<span class="terminal-preview-prompt">$</span> npx opencode-agent-kit init --global<br><span style="color: var(--success)">  ✅</span> <span style="color: var(--text-primary)">opencode-agent-kit v1.3.9 installed globally</span>';
           }
         }
 

package.json

@@ -1,6 +1,6 @@
 {
   "name": "opencode-agent-kit",
-  "version": "1.3.8",
+  "version": "1.3.9",
   "description": "Multi-stack OpenCode agent toolkit — 33+ specialized AI agents, 200+ skills, 46 commands, 8 MCP servers (Nuxt, React, Node.js, Laravel, CI3, Android, Flutter, DevOps, SEO, SonarQube, and more)",
   "type": "module",
   "bin": {