delimit-cli 4.1.48 → 4.1.49

package/CHANGELOG.md

@@ -1,5 +1,23 @@
 # Changelog
 
+## [4.1.49] - 2026-04-09
+
+### Fixed (full preservation audit follow-up to 4.1.48)
+- **Project `.claude/settings.json` hooks clobber** — `installClaudeHooks` was replacing the project-level `.claude/settings.json` hooks object with the merged-with-global config, propagating global hooks into every project file and wiping any project-local hooks the user had set. Now merges only Delimit-owned hook groups (entries whose command contains `delimit`) into existing project hooks; project-specific user hooks survive.
+- **Gemini `general.defaultApprovalMode` clobber** — `delimit-cli setup` was force-setting Gemini's `defaultApprovalMode` to `auto_edit` on every run, overwriting whatever the user had chosen (e.g. `manual`). Now only sets it when missing.
+- **`~/.claude.json` MCP hooks replacement** — `lib/hooks-installer.js` (opt-in via `delimit-cli hooks install`) replaced `preCommand` / `postCommand` / `authentication` / `audit` keys on every install. Now only fills in missing keys, preserving any user-chosen MCP hook commands.
+
+### Added
+- **`tests/setup-no-clobber.test.js`** — dedicated regression suite that runs setup helpers against synthetic fresh-user HOME directories with pre-populated user customizations (project hooks, Gemini approval mode, custom MCP hook commands) and asserts none get clobbered. 5 tests, all passing.
+
+### Audit results
+- Audited every `fs.writeFileSync` in `bin/delimit-setup.js`, `lib/cross-model-hooks.js`, `lib/hooks-installer.js`, `adapters/cursor-rules.js`, and `scripts/postinstall.js`.
+- All remaining writes are either delimit-owned (shims, hook scripts, generated `delimit.md`), guarded by `!fs.existsSync` (models.json, social_target_config.json, codex empty file), or surgical merges that preserve user content (`.mcp.json` mcpServers, `.claude/settings.json` allowList, `.codex/config.toml` mcp_servers.delimit block, `.cursor/mcp.json` mcpServers, rc-file PATH append).
+- The full preservation contract is now: `delimit-cli setup` may safely run on any user machine, including via the shim auto-update flow, without destroying user state. New installs and upgrades are equivalent for everything except delimit-owned files.
+
+### Tests
+- 129/129 passing (was 124).
+
 ## [4.1.48] - 2026-04-09
 
 ### Fixed

package/bin/delimit-setup.js

@@ -430,9 +430,12 @@ async function main() {
                 cwd: path.join(DELIMIT_HOME, 'server'),
                 env: { PYTHONPATH: path.join(DELIMIT_HOME, 'server') }
             };
-            // Auto-approve all tools — users should not be prompted for every Delimit call
+            // Auto-approve all tools — users should not be prompted for every Delimit call.
+            // Only set if missing — never clobber the user's chosen approval mode on upgrade.
             if (!geminiConfig.general) geminiConfig.general = {};
-            geminiConfig.general.defaultApprovalMode = 'auto_edit';
+            if (!geminiConfig.general.defaultApprovalMode) {
+                geminiConfig.general.defaultApprovalMode = 'auto_edit';
+            }
             fs.writeFileSync(GEMINI_CONFIG, JSON.stringify(geminiConfig, null, 2));
             if (geminiExisted) {
                 await logp(`  ${green('✓')} Updated Delimit paths in Gemini CLI config`);

package/lib/cross-model-hooks.js

@@ -577,14 +577,38 @@ echo ""
     const configJson = JSON.stringify(config, null, 2);
     for (const target of writeTargets) {
         try {
-            // For project settings, merge hooks into existing config
-            if (target !== configPath && fs.existsSync(target)) {
-                const existing = JSON.parse(fs.readFileSync(target, 'utf-8'));
-                existing.hooks = config.hooks;
-                fs.writeFileSync(target, JSON.stringify(existing, null, 2));
-            } else {
+            if (target === configPath) {
+                // Global ~/.claude/settings.json: write the merged config we built
                 fs.writeFileSync(target, configJson);
+                continue;
+            }
+
+            // Project settings (.claude/settings.json in cwd): merge ONLY the
+            // Delimit-added hook entries into existing project hooks. Never
+            // overwrite the project's own hook entries with global ones.
+            // Previous behavior (`existing.hooks = config.hooks`) propagated
+            // every global hook into project files, wiping project-local hooks
+            // and leaking unrelated user customizations across repos.
+            let existing = {};
+            if (fs.existsSync(target)) {
+                try { existing = JSON.parse(fs.readFileSync(target, 'utf-8')); } catch { existing = {}; }
+            }
+            if (!existing.hooks) existing.hooks = {};
+
+            for (const [event, groups] of Object.entries(config.hooks || {})) {
+                if (!Array.isArray(groups)) continue;
+                if (!existing.hooks[event]) existing.hooks[event] = [];
+                for (const group of groups) {
+                    const cmds = (group.hooks || []).map(h => h.command || '');
+                    // Only propagate Delimit-owned hook groups to project files
+                    if (!cmds.some(c => c.includes('delimit'))) continue;
+                    const alreadyHas = existing.hooks[event].some(eg =>
+                        (eg.hooks || []).some(h => cmds.includes(h.command))
+                    );
+                    if (!alreadyHas) existing.hooks[event].push(group);
+                }
             }
+            fs.writeFileSync(target, JSON.stringify(existing, null, 2));
         } catch {}
     }
     return changes;

package/lib/hooks-installer.js

@@ -185,29 +185,37 @@ class DelimitHooksInstaller {
     
     async configureClaudeCode() {
         const claudeConfigPath = path.join(process.env.HOME, '.claude.json');
-        
+
         if (fs.existsSync(claudeConfigPath)) {
             try {
                 const config = JSON.parse(fs.readFileSync(claudeConfigPath, 'utf8'));
-                
-                // Add Delimit governance hooks
+
+                // Preserve any existing hooks the user has set. Only fill in
+                // Delimit MCP hooks if those specific keys are missing —
+                // never overwrite a user-chosen preCommand/postCommand.
                 if (!config.hooks) {
                     config.hooks = {};
                 }
-                
-                config.hooks.preCommand = path.join(this.mcpHooksDir, 'pre-mcp-call');
-                config.hooks.postCommand = path.join(this.mcpHooksDir, 'post-mcp-call');
-                config.hooks.authentication = path.join(this.mcpHooksDir, 'mcp-auth');
-                config.hooks.audit = path.join(this.mcpHooksDir, 'mcp-audit');
-                
-                // Add Delimit governance settings
+                const delimitHooks = {
+                    preCommand: path.join(this.mcpHooksDir, 'pre-mcp-call'),
+                    postCommand: path.join(this.mcpHooksDir, 'post-mcp-call'),
+                    authentication: path.join(this.mcpHooksDir, 'mcp-auth'),
+                    audit: path.join(this.mcpHooksDir, 'mcp-audit'),
+                };
+                for (const [key, value] of Object.entries(delimitHooks)) {
+                    if (!config.hooks[key]) {
+                        config.hooks[key] = value;
+                    }
+                }
+
+                // Add Delimit governance settings (own namespace, safe to set)
                 config.delimitGovernance = {
                     enabled: true,
                     agent: 'http://127.0.0.1:7823',
                     mode: 'auto',
                     hooks: this.mcpHooks.map(h => path.join(this.mcpHooksDir, h))
                 };
-                
+
                 fs.writeFileSync(claudeConfigPath, JSON.stringify(config, null, 2));
                 console.log(chalk.green('  ✓ Claude Code configuration updated'));
             } catch (e) {

package/package.json

@@ -1,7 +1,7 @@
 {
   "name": "delimit-cli",
   "mcpName": "io.github.delimit-ai/delimit-mcp-server",
-  "version": "4.1.48",
+  "version": "4.1.49",
   "description": "Unify Claude Code, Codex, Cursor, and Gemini CLI with persistent context, governance, and multi-model debate.",
   "main": "index.js",
   "files": [
@@ -35,7 +35,7 @@
     "postinstall": "node scripts/postinstall.js",
     "sync-gateway": "bash scripts/sync-gateway.sh",
     "prepublishOnly": "bash scripts/publish-ci-guard.sh && npm run sync-gateway && bash scripts/security-check.sh",
-    "test": "node --test tests/setup-onboarding.test.js tests/setup-matrix.test.js tests/config-export-import.test.js tests/cross-model-hooks.test.js tests/golden-path.test.js tests/v420-features.test.js"
+    "test": "node --test tests/setup-onboarding.test.js tests/setup-matrix.test.js tests/setup-no-clobber.test.js tests/config-export-import.test.js tests/cross-model-hooks.test.js tests/golden-path.test.js tests/v420-features.test.js"
   },
   "keywords": [
     "openapi",