diff --git a/cmd/init.go b/cmd/init.go
index 55e2d83..c514da7 100644
--- a/cmd/init.go
+++ b/cmd/init.go
@@ -4,6 +4,7 @@ import (
 	"fmt"
 	"os"
 	"path/filepath"
+	"strings"
 
 	"github.com/robmorgan/metamorph/internal/constants"
 	"github.com/spf13/cobra"
@@ -116,13 +117,37 @@ Add project-specific instructions for your agents here.
 			fmt.Printf("  Created %s/\n", d)
 		}
 
-		// Write .gitignore.
+		// Append entries to .gitignore (create if missing, never overwrite).
 		gitignorePath := filepath.Join(absDir, ".gitignore")
-		gitignoreContent := ".metamorph/\nagent_logs/\n"
-		if err := os.WriteFile(gitignorePath, []byte(gitignoreContent), 0644); err != nil {
-			return fmt.Errorf("failed to write .gitignore: %w", err)
+		requiredEntries := []string{".metamorph/", "agent_logs/"}
+		existing, _ := os.ReadFile(gitignorePath)
+		existingStr := string(existing)
+		var toAdd []string
+		for _, entry := range requiredEntries {
+			if !strings.Contains(existingStr, entry) {
+				toAdd = append(toAdd, entry)
+			}
+		}
+		if len(toAdd) > 0 {
+			f, err := os.OpenFile(gitignorePath, os.O_APPEND|os.O_CREATE|os.O_WRONLY, 0644)
+			if err != nil {
+				return fmt.Errorf("failed to open .gitignore: %w", err)
+			}
+			// Add a newline before appending if the file doesn't end with one.
+			if len(existingStr) > 0 && !strings.HasSuffix(existingStr, "\n") {
+				_, _ = f.WriteString("\n")
+			}
+			for _, entry := range toAdd {
+				if _, err := f.WriteString(entry + "\n"); err != nil {
+					_ = f.Close()
+					return fmt.Errorf("failed to write .gitignore entry: %w", err)
+				}
+			}
+			_ = f.Close()
+			fmt.Println("  Updated .gitignore")
+		} else {
+			fmt.Println("  .gitignore already up to date")
 		}
-		fmt.Println("  Created .gitignore")
 
 		fmt.Printf("\nProject %q initialized successfully!\n\n", projectName)
 		fmt.Println("Next steps:")
diff --git a/internal/gitops/gitops.go b/internal/gitops/gitops.go
index f3747e8..ee8114a 100644
--- a/internal/gitops/gitops.go
+++ b/internal/gitops/gitops.go
@@ -206,8 +206,8 @@ func SyncToProjectDir(upstreamPath, projectDir string) (string, error) {
 		return "", fmt.Errorf("gitops: fetch failed: %w", err)
 	}
 
-	// Merge FETCH_HEAD.
-	if _, err := git(projectDir, "merge", "FETCH_HEAD", "--no-edit"); err != nil {
+	// Merge FETCH_HEAD, auto-resolving conflicts in favor of upstream (agent work).
+	if _, err := git(projectDir, "merge", "-X", "theirs", "FETCH_HEAD", "--no-edit"); err != nil {
 		if _, abortErr := git(projectDir, "merge", "--abort"); abortErr != nil {
 			slog.Warn("gitops: failed to abort merge", "error", abortErr)
 		}
diff --git a/internal/gitops/gitops_test.go b/internal/gitops/gitops_test.go
index 15d10f9..7e324c4 100644
--- a/internal/gitops/gitops_test.go
+++ b/internal/gitops/gitops_test.go
@@ -674,7 +674,7 @@ func TestSyncToProjectDir(t *testing.T) {
 		}
 	})
 
-	t.Run("aborts merge on conflict", func(t *testing.T) {
+	t.Run("auto-resolves conflict in favor of upstream", func(t *testing.T) {
 		projectDir, upstreamPath := setupUpstream(t)
 
 		// Push a conflicting change via upstream (simulating an agent).
@@ -713,19 +713,19 @@ func TestSyncToProjectDir(t *testing.T) {
 			t.Fatal(err)
 		}
 
-		// Sync should fail due to merge conflict.
+		// Sync should auto-resolve the conflict in favor of upstream (theirs).
 		_, err := SyncToProjectDir(upstreamPath, projectDir)
-		if err == nil {
-			t.Fatal("expected merge conflict error")
-		}
-		if !strings.Contains(err.Error(), "merge failed") {
-			t.Errorf("expected 'merge failed' in error, got: %v", err)
+		if err != nil {
+			t.Fatalf("expected auto-resolved merge, got error: %v", err)
 		}
 
-		// Verify merge was aborted — MERGE_HEAD should not exist.
-		mergeHead := filepath.Join(projectDir, ".git", "MERGE_HEAD")
-		if _, err := os.Stat(mergeHead); err == nil {
-			t.Error("MERGE_HEAD exists — merge was not aborted")
+		// Verify upstream version won.
+		content, err := os.ReadFile(filepath.Join(projectDir, "conflict.txt"))
+		if err != nil {
+			t.Fatal(err)
+		}
+		if string(content) != "agent version\n" {
+			t.Errorf("expected upstream content to win, got: %q", string(content))
 		}
 	})
 }