fix: Add git worktree support for Docker environments

- Add _is_git_worktree() method to detect worktree environments
- Wrap git fetch in try-catch to handle GitCommandError gracefully
- Add informative warning messages for worktree scenarios
- Update exception handling to catch both InvalidGitRepositoryError and GitCommandError
- Add comprehensive unit tests for worktree detection and error handling

Fixes #6455

megalinter/MegaLinter.py

@@ -701,7 +701,7 @@ def collect_files(self):
             # List files using git diff
             try:
                 all_files = self.list_files_git_diff()
-            except git.InvalidGitRepositoryError as git_err:
+            except (git.InvalidGitRepositoryError, git.exc.GitCommandError) as git_err:
                 logging.warning(
                     "Unable to list updated files from git diff. Switch to VALIDATE_ALL_CODE_BASE=true"
                 )
@@ -788,12 +788,45 @@ def collect_files(self):
             if len(linter.files) == 0 and linter.lint_all_files is False:
                 linter.is_active = False
 
+    def _is_git_worktree(self, repo):
+        """
+        Detect if the current git repository is a worktree.
+
+        In a worktree, the .git directory is actually a file containing
+        a gitdir reference to the main repository's worktrees directory.
+
+        Args:
+            repo: GitPython Repo object
+
+        Returns:
+            bool: True if this is a worktree, False otherwise
+        """
+        try:
+            git_dir = repo.git_dir
+            # Check if .git is a file (worktree) or directory (regular repo)
+            git_path = os.path.join(repo.working_dir, '.git')
+            if os.path.isfile(git_path):
+                # It's a worktree - .git is a file containing gitdir reference
+                return True
+            # Also check if git_dir contains 'worktrees' in the path
+            if 'worktrees' in git_dir:
+                return True
+        except Exception as e:
+            logging.debug(f"Error checking for worktree: {str(e)}")
+        return False
+
     def list_files_git_diff(self):
         # List all updated files from git
         logging.info(
             "Listing updated files in [" + self.github_workspace + "] using git diff."
         )
         repo = git.Repo(os.path.realpath(self.github_workspace))
+
+        # Check if we're in a git worktree
+        is_worktree = self._is_git_worktree(repo)
+        if is_worktree:
+            logging.info("Detected git worktree environment")
+
         # Add auth header if necessary
         if config.get(self.request_id, "GIT_AUTHORIZATION_BEARER", "") != "":
             auth_bearer = "Authorization: Bearer " + config.get(
@@ -810,7 +843,25 @@ def list_files_git_diff(self):
             )
             local_ref = f"refs/remotes/{default_branch_remote}"
             # Try to fetch default_branch from origin, because it isn't cached locally.
-            repo.git.fetch("origin", f"{remote_ref}:{local_ref}")
+            try:
+                repo.git.fetch("origin", f"{remote_ref}:{local_ref}")
+            except git.exc.GitCommandError as fetch_err:
+                # Handle worktree and other fetch errors gracefully
+                logging.warning(
+                    f"Unable to fetch {remote_ref} from origin: {str(fetch_err)}"
+                )
+                if is_worktree:
+                    logging.warning(
+                        "Git worktree detected - this is a known issue when running in Docker. "
+                        "The worktree's .git file contains an absolute path that is invalid inside the container. "
+                        "Continuing without fetch - ensure your repository is up-to-date before running MegaLinter."
+                    )
+                else:
+                    logging.warning(
+                        "Continuing without fetch - this may result in comparing against a stale branch. "
+                        "Consider setting VALIDATE_ALL_CODEBASE=true to avoid git operations."
+                    )
+                # Continue without the fetch - use whatever refs are available
         # Make git diff to list files (and exclude symlinks)
         try:
             # Use optimized way from https://github.com/oxsecurity/megalinter/pull/3472

megalinter/tests/test_megalinter/worktree_test.py

@@ -0,0 +1,166 @@
+#!/usr/bin/env python3
+"""
+Unit tests for Git worktree handling in MegaLinter
+
+"""
+import os
+import tempfile
+import unittest
+from unittest.mock import MagicMock, Mock, patch
+
+import git
+
+from megalinter import Megalinter
+
+
+class worktree_test(unittest.TestCase):
+    """Test Git worktree detection and error handling"""
+
+    def test_is_git_worktree_detection_for_regular_repo(self):
+        """Test that a regular repository is NOT detected as a worktree"""
+        # Create a mock repo that represents a regular repository
+        mock_repo = Mock()
+        mock_repo.git_dir = "/path/to/repo/.git"
+        mock_repo.working_dir = "/path/to/repo"
+
+        # Create a temporary directory to simulate a regular repo
+        with tempfile.TemporaryDirectory() as tmpdir:
+            git_dir = os.path.join(tmpdir, ".git")
+            os.makedirs(git_dir)
+
+            mock_repo.working_dir = tmpdir
+            mock_repo.git_dir = git_dir
+
+            # Create MegaLinter instance
+            megalinter = Megalinter({"workspace": tmpdir, "cli": False})
+
+            # Test worktree detection
+            is_worktree = megalinter._is_git_worktree(mock_repo)
+
+            self.assertFalse(
+                is_worktree,
+                "Regular repository should NOT be detected as a worktree"
+            )
+
+    def test_is_git_worktree_detection_for_worktree_file(self):
+        """Test that a worktree (with .git as a file) IS detected"""
+        # Create a mock repo that represents a worktree
+        mock_repo = Mock()
+        mock_repo.git_dir = "/path/to/repo/.git/worktrees/my-worktree"
+
+        # Create a temporary directory to simulate a worktree
+        with tempfile.TemporaryDirectory() as tmpdir:
+            # Create .git as a FILE (worktree indicator)
+            git_file = os.path.join(tmpdir, ".git")
+            with open(git_file, "w") as f:
+                f.write("gitdir: /path/to/repo/.git/worktrees/my-worktree\n")
+
+            mock_repo.working_dir = tmpdir
+
+            # Create MegaLinter instance
+            megalinter = Megalinter({"workspace": tmpdir, "cli": False})
+
+            # Test worktree detection
+            is_worktree = megalinter._is_git_worktree(mock_repo)
+
+            self.assertTrue(
+                is_worktree,
+                "Worktree (with .git file) should be detected as a worktree"
+            )
+
+    def test_is_git_worktree_detection_by_path(self):
+        """Test that a worktree is detected by 'worktrees' in git_dir path"""
+        # Create a mock repo with 'worktrees' in the path
+        mock_repo = Mock()
+        mock_repo.git_dir = "/path/to/repo/.git/worktrees/my-worktree"
+        mock_repo.working_dir = "/path/to/worktree"
+
+        # Create a temporary directory
+        with tempfile.TemporaryDirectory() as tmpdir:
+            mock_repo.working_dir = tmpdir
+            git_dir_path = os.path.join(tmpdir, ".git")
+            os.makedirs(git_dir_path)
+
+            # Override git_dir to have 'worktrees' in path
+            mock_repo.git_dir = "/main/.git/worktrees/test"
+
+            # Create MegaLinter instance
+            megalinter = Megalinter({"workspace": tmpdir, "cli": False})
+
+            # Test worktree detection
+            is_worktree = megalinter._is_git_worktree(mock_repo)
+
+            self.assertTrue(
+                is_worktree,
+                "Worktree should be detected by 'worktrees' in git_dir path"
+            )
+
+    @patch("git.Repo")
+    def test_git_fetch_error_handling_in_worktree(self, mock_repo_class):
+        """Test that git fetch errors are properly handled in worktrees"""
+        # Create a temporary directory
+        with tempfile.TemporaryDirectory() as tmpdir:
+            # Create .git as a file to simulate worktree
+            git_file = os.path.join(tmpdir, ".git")
+            with open(git_file, "w") as f:
+                f.write("gitdir: /main/.git/worktrees/test\n")
+
+            # Mock the Repo object
+            mock_repo_instance = Mock()
+            mock_repo_instance.git_dir = "/main/.git/worktrees/test"
+            mock_repo_instance.working_dir = tmpdir
+            mock_repo_instance.refs = []
+
+            # Mock git.fetch to raise GitCommandError
+            mock_repo_instance.git.fetch.side_effect = git.exc.GitCommandError(
+                "git fetch",
+                128,
+                stderr="fatal: not a git repository: /host/path/.git/worktrees/test"
+            )
+
+            mock_repo_class.return_value = mock_repo_instance
+
+            # Create MegaLinter instance
+            megalinter = Megalinter({"workspace": tmpdir, "cli": False})
+
+            # Try to list files using git diff - should not raise an exception
+            try:
+                # This should handle the error gracefully
+                files = megalinter.list_files_git_diff()
+                # If we get here, the error was handled
+                self.assertTrue(
+                    True,
+                    "Git fetch error should be caught and handled"
+                )
+            except git.exc.GitCommandError:
+                self.fail(
+                    "GitCommandError should be caught and handled, not raised"
+                )
+
+    def test_worktree_detection_handles_exceptions(self):
+        """Test that worktree detection handles exceptions gracefully"""
+        # Create a mock repo that raises an exception
+        mock_repo = Mock()
+        mock_repo.git_dir = Mock(side_effect=Exception("Test exception"))
+
+        with tempfile.TemporaryDirectory() as tmpdir:
+            # Create MegaLinter instance
+            megalinter = Megalinter({"workspace": tmpdir, "cli": False})
+
+            # Test worktree detection - should not raise exception
+            try:
+                is_worktree = megalinter._is_git_worktree(mock_repo)
+                # Should return False when exception occurs
+                self.assertFalse(
+                    is_worktree,
+                    "Should return False when exception occurs during detection"
+                )
+            except Exception:
+                self.fail(
+                    "Worktree detection should handle exceptions gracefully"
+                )
+
+
+if __name__ == "__main__":
+    unittest.main()
+