From 857251f4e069d56942542b44ddf3e5d72d4a2220 Mon Sep 17 00:00:00 2001
From: NagyVikt <nagy.viktordp@gmail.com>
Date: Fri, 17 Apr 2026 15:23:43 +0200
Subject: [PATCH] Keep gx doctor repair-first and normalize worktree status
 checks

Users reported gx doctor failing hard on package script mismatches even when repair could resolve them. Root cause was a duplicate legacy doctor definition overriding the active repair-first flow in the command path.

This patch keeps the repair-first doctor as the only active doctor command, and aligns worktree dirty detection with normal untracked-file mode using git status --porcelain --untracked-files=normal --.

Constraint: Preserve existing doctor command UX and output contract for guarded repos
Rejected: Delete legacy doctor audit block entirely in this hotfix | larger refactor than needed for immediate behavior fix
Confidence: high
Scope-risk: narrow
Reversibility: clean
Directive: Do not introduce duplicate top-level command handlers with the same function name
Tested: node --check bin/multiagent-safety.js; npm test; node bin/multiagent-safety.js doctor --target /home/deadpool/Documents/recodee
Not-tested: npm publish/install path for this patch version
---
 README.md                |  2 ++
 bin/multiagent-safety.js | 11 +++++++++--
 test/metadata.test.js    | 16 +++++++++++++++-
 3 files changed, 26 insertions(+), 3 deletions(-)

diff --git a/README.md b/README.md
index ec8bee1..3d6aa2c 100644
--- a/README.md
+++ b/README.md
@@ -375,6 +375,8 @@ npm pack --dry-run
 ### v5.0.16
 
 - Fixed `gx doctor` runtime crash (`parseDoctorArgs is not defined`) by restoring the doctor argument parser for `--target` and `--strict`.
+- Fixed `gx doctor` command routing so the repair-first doctor flow remains the active command path (duplicate legacy doctor definition no longer overrides it).
+- Updated worktree change detection to run `git status --porcelain --untracked-files=normal --` for consistent normal untracked-file behavior.
 - Added regression coverage that asserts the doctor parser function exists in `bin/multiagent-safety.js`.
 - Bumped package version from `5.0.15` to `5.0.16`.
 
diff --git a/bin/multiagent-safety.js b/bin/multiagent-safety.js
index 1aa45c0..14aed11 100755
--- a/bin/multiagent-safety.js
+++ b/bin/multiagent-safety.js
@@ -2117,7 +2117,14 @@ function mapWorktreePathsByBranch(repoRoot) {
 }
 
 function hasSignificantWorkingTreeChanges(worktreePath) {
-  const result = run('git', ['-C', worktreePath, 'status', '--porcelain']);
+  const result = run('git', [
+    '-C',
+    worktreePath,
+    'status',
+    '--porcelain',
+    '--untracked-files=normal',
+    '--',
+  ]);
   if (result.status !== 0) {
     return true;
   }
@@ -4659,7 +4666,7 @@ function initWorkspace(rawArgs) {
   }
 }
 
-function doctor(rawArgs) {
+function doctorAudit(rawArgs) {
   const options = parseDoctorArgs(rawArgs);
   const repoRoot = resolveRepoRoot(options.target);
   const failures = [];
diff --git a/test/metadata.test.js b/test/metadata.test.js
index 7ca4b1e..084eddf 100644
--- a/test/metadata.test.js
+++ b/test/metadata.test.js
@@ -80,5 +80,19 @@ test('doctor CLI parser exists to prevent runtime ReferenceError regressions', (
   const cliPath = path.join(repoRoot, 'bin', 'multiagent-safety.js');
   const cliSource = fs.readFileSync(cliPath, 'utf8');
   assert.match(cliSource, /function parseDoctorArgs\(rawArgs\)/);
-  assert.match(cliSource, /const options = parseDoctorArgs\(rawArgs\);/);
+  assert.match(cliSource, /function doctorAudit\(rawArgs\)/);
+});
+
+test('active doctor command remains single-source and runs the repair-first path', () => {
+  const cliPath = path.join(repoRoot, 'bin', 'multiagent-safety.js');
+  const cliSource = fs.readFileSync(cliPath, 'utf8');
+  const doctorDefs = cliSource.match(/function doctor\(rawArgs\)/g) || [];
+  assert.equal(doctorDefs.length, 1, 'doctor() must not be duplicated');
+  assert.match(cliSource, /printOperations\('Doctor\/fix', fixPayload, options\.dryRun\);/);
+});
+
+test('worktree-change detection uses normal untracked-file mode', () => {
+  const cliPath = path.join(repoRoot, 'bin', 'multiagent-safety.js');
+  const cliSource = fs.readFileSync(cliPath, 'utf8');
+  assert.match(cliSource, /'status',\s*'--porcelain',\s*'--untracked-files=normal',\s*'--'/s);
 });