Fix: Change default JSONL filename from beads.jsonl to issues.jsonl

The canonical beads database name is issues.jsonl. Tens of thousands of users
have issues.jsonl, and beads.jsonl was only used by the Beads project itself
due to git history pollution.

Changes:
- Updated bd doctor to warn about beads.jsonl instead of issues.jsonl
- Changed default config from beads.jsonl to issues.jsonl
- Reversed precedence in checkGitForIssues to prefer issues.jsonl
- Updated git merge driver config to use issues.jsonl
- Updated all tests to expect issues.jsonl as the default

issues.jsonl is now the canonical default; beads.jsonl is legacy

🤖 Generated with [Claude Code](https://claude.com/claude-code)

Co-Authored-By: Claude <noreply@anthropic.com>

cmd/bd/init_test.go

@@ -526,7 +526,7 @@ func TestInitMergeDriverAutoConfiguration(t *testing.T) {
 		if err != nil {
 			t.Fatalf("Failed to read .gitattributes: %v", err)
 		}
-		if !strings.Contains(string(content), ".beads/beads.jsonl merge=beads") {
+		if !strings.Contains(string(content), ".beads/issues.jsonl merge=beads") {
 			t.Error(".gitattributes should contain merge driver configuration")
 		}
 	})
@@ -633,7 +633,7 @@ func TestInitMergeDriverAutoConfiguration(t *testing.T) {
 
 		// Create .gitattributes with merge driver
 		gitattrsPath := filepath.Join(tmpDir, ".gitattributes")
-		initialContent := "# Existing config\n.beads/beads.jsonl merge=beads\n"
+		initialContent := "# Existing config\n.beads/issues.jsonl merge=beads\n"
 		if err := os.WriteFile(gitattrsPath, []byte(initialContent), 0644); err != nil {
 			t.Fatalf("Failed to create .gitattributes: %v", err)
 		}
@@ -661,7 +661,7 @@ func TestInitMergeDriverAutoConfiguration(t *testing.T) {
 
 		contentStr := string(content)
 		// Count occurrences - should only appear once
-		count := strings.Count(contentStr, ".beads/beads.jsonl merge=beads")
+		count := strings.Count(contentStr, ".beads/issues.jsonl merge=beads")
 		if count != 1 {
 			t.Errorf("Expected .gitattributes to contain merge config exactly once, found %d times", count)
 		}
@@ -727,13 +727,13 @@ func TestInitMergeDriverAutoConfiguration(t *testing.T) {
 		}
 
 		// Should contain beads config
-		if !strings.Contains(contentStr, ".beads/beads.jsonl merge=beads") {
+		if !strings.Contains(contentStr, ".beads/issues.jsonl merge=beads") {
 			t.Error(".gitattributes should contain beads merge config")
 		}
 
 		// Beads config should come after existing content
 		txtIdx := strings.Index(contentStr, "*.txt")
-		beadsIdx := strings.Index(contentStr, ".beads/beads.jsonl")
+		beadsIdx := strings.Index(contentStr, ".beads/issues.jsonl")
 		if txtIdx >= beadsIdx {
 			t.Error("Beads config should be appended after existing content")
 		}