fix: Remove YAML usage, standardize on JSON/TOML

- Delete 5 legacy .formula.yaml files (have .toml replacements)
- Remove unused FileConfigYAML constant
- Add TODO for beads config.yaml → config.json migration (bd-10wg)
- Update docs to use JSON examples instead of yaml code blocks
- Change plugin frontmatter from YAML to TOML in docs
- Add .toml to code file detection in branch_check.go

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

Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>

internal/doctor/branch_check.go

@@ -273,8 +273,9 @@ func (c *BeadsSyncOrphanCheck) Run(ctx *CheckContext) *CheckResult {
 		}
 		// Check if it's a code file
 		if strings.HasSuffix(f, ".go") || strings.HasSuffix(f, ".md") ||
+			strings.HasSuffix(f, ".toml") || strings.HasSuffix(f, ".json") ||
 			strings.HasSuffix(f, ".yaml") || strings.HasSuffix(f, ".yml") ||
-			strings.HasSuffix(f, ".json") || strings.HasSuffix(f, ".tmpl") {
+			strings.HasSuffix(f, ".tmpl") {
 			codeFiles = append(codeFiles, f)
 		}
 	}