feat(coding-agent): added todo_write tool, persistent todo panel, grouped Read display, and refactored prompts

- Added todo_write tool for creating and managing structured task lists during coding sessions.
- Added persistent todo panel above the editor that displays task progress with Ctrl+T toggle.
- Added grouped display for consecutive Read tool calls in a compact tree view.
- Changed system prompt to use more direct, field-oriented language with emphasis on verification and assumptions.
- Changed Ctrl+Enter to insert newline when not streaming, and Ctrl+T from toggling thinking blocks to toggling todo list.
- Replaced yaml package dependency with Bun's built-in YAML parser and extracted frontmatter parsing to dedicated module.

packages/coding-agent/src/discovery/github.ts

@@ -18,7 +18,8 @@ import { readFile } from "../capability/fs";
 import { registerProvider } from "../capability/index";
 import { type Instruction, instructionCapability } from "../capability/instruction";
 import type { LoadContext, LoadResult, SourceMeta } from "../capability/types";
-import { calculateDepth, createSourceMeta, getProjectPath, loadFilesFromDir, parseFrontmatter } from "./helpers";
+import { parseFrontmatter } from "../core/frontmatter";
+import { calculateDepth, createSourceMeta, getProjectPath, loadFilesFromDir } from "./helpers";
 
 const PROVIDER_ID = "github";
 const DISPLAY_NAME = "GitHub Copilot";