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.go

@@ -812,12 +812,14 @@ func installMergeDriver() error {
 	}
 
 	// Check if beads merge driver is already configured
-	hasBeadsMerge := strings.Contains(existingContent, ".beads/beads.jsonl") &&
+	// Check for either pattern (issues.jsonl is canonical, beads.jsonl is legacy)
+	hasBeadsMerge := (strings.Contains(existingContent, ".beads/issues.jsonl") ||
+		strings.Contains(existingContent, ".beads/beads.jsonl")) &&
 		strings.Contains(existingContent, "merge=beads")
 
 	if !hasBeadsMerge {
-		// Append beads merge driver configuration
-		beadsMergeAttr := "\n# Use bd merge for beads JSONL files\n.beads/beads.jsonl merge=beads\n"
+		// Append beads merge driver configuration (issues.jsonl is canonical)
+		beadsMergeAttr := "\n# Use bd merge for beads JSONL files\n.beads/issues.jsonl merge=beads\n"
 
 		newContent := existingContent
 		if !strings.HasSuffix(newContent, "\n") && len(newContent) > 0 {