Preserve unrelated host MCP settings and managed ownership

src/claude/init.ts

@@ -1,4 +1,4 @@
-import { mkdirSync, writeFileSync, readFileSync, chmodSync } from 'node:fs';
+import { mkdirSync, writeFileSync, chmodSync } from 'node:fs';
 import { join, dirname } from 'node:path';
 import { homedir } from 'node:os';
 import { execFileSync } from 'node:child_process';
@@ -10,6 +10,7 @@ import { claudeDistDir } from './paths.js';
 import { mergeJsonKey, serverEntry, type McpWrite } from '../hosts/mcp-config.js';
 import { hasGraftIndex } from '../graph/root.js';
 import type { PlannedWrite } from '../hosts/plan.js';
+import { readJsonObject } from '../hosts/config-write.js';
 
 /**
  * The files `runInit` writes — pure, no writes, so `--dry-run` and the picker
@@ -67,12 +68,13 @@ export function runInit(
   // Same list `--dry-run` and the picker report, so the two can't drift apart.
   const [settings, statusline, hooks, skill, mcpTarget] = claudeTargets(dir).map((t) => t.path);
 
-  mkdirSync(dirname(statusline), { recursive: true });
-
   const settingsPath = settings;
-  let existing: Record<string, any> = {};
-  try { existing = JSON.parse(readFileSync(settingsPath, 'utf8')); } catch { /* none/invalid → start fresh */ }
-  const { merged, warnings } = mergeGraftSettings(existing, { statusline: opts.statusline });
+  const loaded = readJsonObject(settingsPath);
+  if (loaded === 'unparseable') {
+    throw new Error(`Cannot initialize Graft: ${settingsPath} is not a readable JSON object; existing settings left unchanged.`);
+  }
+  const { merged, warnings } = mergeGraftSettings(loaded.root, { statusline: opts.statusline });
+  mkdirSync(dirname(statusline), { recursive: true });
   writeFileSync(settingsPath, `${JSON.stringify(merged, null, 2)}\n`);
 
   const sl = statusline;

src/hosts/retract.ts

@@ -484,12 +484,13 @@ export function planRetract(repo: string, opts: RetractOpts = {}): Retraction[]
 }
 
 /**
- * Remove graft's contribution from every target. Reports every target it
+ * Report graft's contribution by default; remove it only with `apply: true`.
+ * Reports every target it
  * considered, including the ones that were already clean, so a caller can show
  * either the full sweep or just what changed.
  */
 export function runRetract(repo: string, opts: RetractOpts = {}): Retraction[] {
-  const apply = opts.apply !== false;
+  const apply = opts.apply === true;
   return targets(repo, opts).map(({ run, ...t }) => ({ ...t, action: run(apply) }));
 }
 

test/graft-preservation.test.ts

@@ -0,0 +1,89 @@
+import { test, after } from 'node:test';
+import assert from 'node:assert/strict';
+import { mkdtempSync, mkdirSync, readFileSync, writeFileSync, readdirSync, existsSync, rmSync } from 'node:fs';
+import { join } from 'node:path';
+import { tmpdir } from 'node:os';
+import { runInit } from '../src/claude/init.js';
+import { runRetract } from '../src/hosts/retract.js';
+
+// Never probe an installed package or start a missing-graph build/provider.
+process.env.GRAFT_MCP_NPX = '1';
+const owned: string[] = [];
+function fresh(): string {
+  const dir = mkdtempSync(join(tmpdir(), 'graft-preservation-'));
+  owned.push(dir);
+  return dir;
+}
+after(() => { for (const dir of owned) rmSync(dir, { recursive: true, force: true }); });
+
+for (const body of ['{ malformed', 'null', '[]', '[{"model":"user"}]', '42', '"user"', 'false']) {
+  test(`invalid project settings ${body} stay byte-identical before any other installation write`, () => {
+    const repo = fresh();
+    const home = fresh();
+    mkdirSync(join(repo, '.claude'));
+    const settings = join(repo, '.claude', 'settings.json');
+    writeFileSync(settings, body);
+    assert.throws(() => runInit(repo, { build: false, global: false, home }), /not a readable JSON object/);
+    assert.equal(readFileSync(settings, 'utf8'), body);
+    assert.deepEqual(readdirSync(join(repo, '.claude')), ['settings.json']);
+    assert.deepEqual(readdirSync(home), []);
+    assert.equal(existsSync(join(repo, '.mcp.json')), false);
+    assert.equal(existsSync(join(repo, 'graft')), false);
+  });
+}
+
+test('missing project settings create normal repo wiring without home or graph writes', () => {
+  const repo = fresh();
+  const home = fresh();
+  const result = runInit(repo, { build: false, global: false, home });
+  const settings = JSON.parse(readFileSync(result.settingsPath, 'utf8'));
+  assert.ok(settings.hooks.Stop);
+  assert.ok(existsSync(join(repo, '.mcp.json')));
+  assert.equal(result.built, false);
+  assert.deepEqual(result.global, []);
+  assert.deepEqual(readdirSync(home), []);
+  assert.equal(existsSync(join(repo, 'graft')), false);
+});
+
+test('valid project settings preserve foreign settings and ordinary foreign handlers', () => {
+  const repo = fresh();
+  const home = fresh();
+  mkdirSync(join(repo, '.claude'));
+  const path = join(repo, '.claude', 'settings.json');
+  const foreign = { matcher: 'Bash', hooks: [{ type: 'command', command: 'inert-foreign-sentinel' }] };
+  writeFileSync(path, JSON.stringify({ model: 'user-choice', statusLine: { command: 'inert-user-bar' },
+    permissions: { deny: ['Bash(inert-deny:*)'], allow: ['Bash(inert-allow:*)'] }, hooks: { Stop: [foreign] } }));
+  const result = runInit(repo, { build: false, global: false, home });
+  const settings = JSON.parse(readFileSync(path, 'utf8'));
+  assert.equal(settings.model, 'user-choice');
+  assert.equal(settings.statusLine.command, 'inert-user-bar');
+  assert.deepEqual(settings.permissions.deny, ['Bash(inert-deny:*)']);
+  assert.ok(settings.permissions.allow.includes('Bash(inert-allow:*)'));
+  assert.deepEqual(settings.hooks.Stop[0], foreign);
+  assert.ok(result.warnings.length);
+  assert.deepEqual(readdirSync(home), []);
+});
+
+for (const apply of [undefined, false, true]) {
+  test(`retract apply=${String(apply)} mutates only on explicit true`, () => {
+    const repo = fresh();
+    const home = fresh();
+    const body = '<!-- graft:start -->\nowned guidance\n<!-- graft:end -->\n';
+    const path = join(repo, 'AGENTS.md');
+    writeFileSync(path, body);
+    mkdirSync(join(home, '.codex'));
+    const config = join(home, '.codex', 'config.toml');
+    const toml = '[mcp_servers.graft]\ncommand = "inert-not-executed"\n';
+    writeFileSync(config, toml);
+    const opts = apply === undefined ? { home } : { home, apply };
+    const reports = runRetract(repo, opts);
+    assert.ok(reports.some((r) => r.path === path && r.action === 'deleted'));
+    if (apply === true) {
+      assert.equal(existsSync(path), false);
+      assert.equal(existsSync(config), false);
+    } else {
+      assert.equal(readFileSync(path, 'utf8'), body);
+      assert.equal(readFileSync(config, 'utf8'), toml);
+    }
+  });
+}