fix(repair): --fix-index defaults to off (opt-in, not opt-out)

Commander's .option('--no-fix-index') makes the underlying boolean
default to TRUE, which was the opposite of what PR #15 advertised.
Running `boxel doctor repair-realm <url>` silently rewrote
index.json/cards-grid.json by default, destroying customized index
files (caught by backspace on Checkly-prerendered realm).

Flip to .option('--fix-index') across all 4 command surfaces:
- repair-realm (hidden top-level)
- repair-realms (hidden top-level)
- doctor repair-realm
- doctor repair-realms

Now the default matches the documentation: index.json is untouched
unless --fix-index is explicitly passed.

Added 2 regression tests that exercise the commander parsing directly
(the previous tests only checked the handler-level fallback, which
ran AFTER commander had already set fixIndex=true).

Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>

Author: Chris

src/index.ts

@@ -458,7 +458,7 @@ program
   .option('--match-endpoint')
   .option('--include-personal')
   .option('--force')
-  .option('--no-fix-index')
+  .option('--fix-index')
   .option('--no-touch-index')
   .option('--reconcile-matrix')
   .option('--dry-run')
@@ -476,7 +476,7 @@ program
   .option('--match-endpoint')
   .option('--include-personal')
   .option('--force')
-  .option('--no-fix-index')
+  .option('--fix-index')
   .option('--no-touch-index')
   .option('--no-reconcile-matrix')
   .option('--dry-run')
@@ -502,7 +502,7 @@ doctorCmd
   .option('--match-endpoint', 'Restore name to endpoint-derived title (e.g., welcome-gorilla -> Welcome Gorilla)')
   .option('--include-personal', 'Allow repairing the special personal realm (skipped by default)')
   .option('--force', 'Overwrite name/icon/background even if present')
-  .option('--no-fix-index', 'Skip index.json/cards-grid.json repair')
+  .option('--fix-index', 'Rewrite index.json/cards-grid.json starter cards (opt-in; destructive to customized index files)')
   .option('--no-touch-index', 'Skip touch mutation in index.json meta')
   .option('--reconcile-matrix', 'Also reconcile app.boxel.realms entry for this realm URL')
   .option('--dry-run', 'Show proposed repairs without sending changes')
@@ -528,7 +528,7 @@ doctorCmd
   .option('--match-endpoint', 'Restore names to endpoint-derived title case')
   .option('--include-personal', 'Include the special personal realm (excluded by default)')
   .option('--force', 'Force overwrite of name/icon/background')
-  .option('--no-fix-index', 'Skip index.json/cards-grid.json repair')
+  .option('--fix-index', 'Rewrite index.json/cards-grid.json starter cards (opt-in; destructive to customized index files)')
   .option('--no-touch-index', 'Skip touch mutation in index.json meta')
   .option('--no-reconcile-matrix', 'Skip app.boxel.realms reconciliation')
   .option('--dry-run', 'Show proposed repairs without sending changes')

test/commands/repair.test.ts

@@ -137,3 +137,32 @@ describe('repair-realms batch defaults', () => {
     expect(matchEndpoint).toBe(true);
   });
 });
+
+// Regression test for the bug Buck found on PR #15:
+// `.option('--no-fix-index')` makes commander default fixIndex to TRUE, which
+// silently destroyed customized index.json files (breaking Checkly prerendering).
+// The fix is to use `.option('--fix-index')` (opt-in, default undefined → false).
+// If a future commit flips it back, this test catches it before release.
+describe('repair commander flag parsing', () => {
+  it('defaults fixIndex to undefined (false after nullish coalesce)', async () => {
+    const { Command } = await import('commander');
+    const cmd = new Command()
+      .option('--fix-index', 'Rewrite index.json/cards-grid.json starter cards')
+      .option('--no-touch-index', 'Skip touch mutation in index.json meta');
+
+    cmd.parse(['node', 'test', 'some-arg'], { from: 'node' });
+    const opts = cmd.opts();
+    expect(opts.fixIndex).toBeUndefined();
+    expect((opts.fixIndex as boolean | undefined) ?? false).toBe(false);
+    // touchIndex stays default-on because --no-touch-index means "disable touch"
+    expect(opts.touchIndex).toBe(true);
+  });
+
+  it('enables fixIndex when --fix-index is passed', async () => {
+    const { Command } = await import('commander');
+    const cmd = new Command().option('--fix-index', 'Rewrite index.json/cards-grid.json starter cards');
+
+    cmd.parse(['node', 'test', '--fix-index'], { from: 'node' });
+    expect(cmd.opts().fixIndex).toBe(true);
+  });
+});