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>

docs/why-these-features.md

@@ -135,10 +135,10 @@ in different repos. Traditional tools don't track this.
 
 **The solution:** Explicit cross-project dependencies:
 
-```yaml
+```
 depends_on:
-  - beads://github/acme/backend/be-456  # Backend API
-  - beads://github/acme/shared/sh-789   # Shared types
+  beads://github/acme/backend/be-456  # Backend API
+  beads://github/acme/shared/sh-789   # Shared types
 ```
 
 **Why it matters:**