fix(setup): use parseJsonc for idempotency check, re-parse tree after each edit

Two fixes from Copilot review on #1031:

1. installClaudeCodeHooks used JSON.parse() for the idempotency check
   on settings.json. If the file contained JSONC comments, parse would
   fail, parsed became null, hasGitnexusHook returned false, and
   duplicate hook entries could be appended. Now uses jsonc-parser's
   parse() instead.

2. mergeHooksJsonc computed insertIndex from the original tree and
   never updated it after applying edits. If two entries targeted the
   same eventName, the second iteration used a stale index and
   overwrote the previously-inserted element. Now re-parses the tree
   inside the loop so each iteration gets a fresh insertion index.

gitnexus/src/cli/setup.ts

@@ -13,7 +13,7 @@ import { execFile, execFileSync } from 'child_process';
 import { promisify } from 'util';
 import { fileURLToPath } from 'url';
 import { glob } from 'glob';
-import { parseTree, modify, applyEdits, ParseError } from 'jsonc-parser';
+import { parseTree, modify, applyEdits, ParseError, parse as parseJsonc } from 'jsonc-parser';
 import { getGlobalDir } from '../storage/repo-manager.js';
 
 const __filename = fileURLToPath(import.meta.url);
@@ -272,7 +272,9 @@ async function mergeHooksJsonc(
   let current = raw;
 
   for (const { eventName, value } of entries) {
-    const hooksNode = tree.children?.find(
+    // Re-parse after each edit to get a fresh insertion index.
+    const currentTree = parseTree(current, []);
+    const hooksNode = currentTree?.children?.find(
       (c) => c.type === 'property' && c.children?.[0]?.value === 'hooks',
     );
     const eventNode = hooksNode?.children?.[1]?.children?.find(
@@ -339,7 +341,7 @@ async function installClaudeCodeHooks(result: SetupResult): Promise<void> {
     const parsed = await (async () => {
       try {
         const r = await fs.readFile(settingsPath, 'utf-8');
-        return JSON.parse(r);
+        return parseJsonc(r);
       } catch {
         return null;
       }

gitnexus/test/unit/setup-jsonc.test.ts

@@ -567,4 +567,25 @@ describe('installClaudeCodeHooks — JSONC preservation', () => {
     const raw = await fs.readFile(settingsPath(), 'utf-8');
     expect(raw).toBe(corrupt);
   });
+
+  it('handles idempotency check with JSONC comments in settings', async () => {
+    const jsonc = `{
+  // settings comment
+  "hooks": {
+    "PreToolUse": [
+      { "matcher": "Grep|Glob|Bash", "hooks": [{ "type": "command", "command": "other-hook" }] }
+    ]
+  }
+}`;
+    await fs.writeFile(settingsPath(), jsonc, 'utf-8');
+
+    const { setupCommand } = await import('../../src/cli/setup.js');
+    await setupCommand();
+
+    const raw = await fs.readFile(settingsPath(), 'utf-8');
+    expect(raw).toContain('settings comment');
+    const config = parseJsonc(raw);
+    expect(config.hooks.PreToolUse.length).toBe(2);
+    expect(config.hooks.PostToolUse.length).toBe(1);
+  });
 });