docs: regenerate AGENTS.md hierarchy via init-deep

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src/shared/AGENTS.md

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+# SHARED UTILITIES KNOWLEDGE BASE
+
+## OVERVIEW
+
+Cross-cutting utility functions used across agents, hooks, tools, and features. Path resolution, config management, text processing, and Claude Code compatibility helpers.
+
+## STRUCTURE
+
+```
+shared/
+├── index.ts              # Barrel export (import { x } from "../shared")
+├── claude-config-dir.ts  # Resolve ~/.claude directory
+├── command-executor.ts   # Shell command execution with variable expansion
+├── config-errors.ts      # Global config error tracking
+├── config-path.ts        # User/project config path resolution
+├── data-path.ts          # XDG data directory resolution
+├── deep-merge.ts         # Type-safe recursive object merging
+├── dynamic-truncator.ts  # Token-aware output truncation
+├── file-reference-resolver.ts  # @filename syntax resolution
+├── file-utils.ts         # Symlink resolution, markdown detection
+├── frontmatter.ts        # YAML frontmatter parsing
+├── hook-disabled.ts      # Check if hook is disabled in config
+├── jsonc-parser.ts       # JSON with Comments parsing
+├── logger.ts             # File-based logging to OS temp
+├── migration.ts          # Legacy name compatibility (omo -> Sisyphus)
+├── model-sanitizer.ts    # Normalize model names
+├── pattern-matcher.ts    # Tool name matching with wildcards
+├── snake-case.ts         # Case conversion for objects
+└── tool-name.ts          # Normalize tool names to PascalCase
+```
+
+## UTILITY CATEGORIES
+
+| Category | Utilities | Used By |
+|----------|-----------|---------|
+| Path Resolution | `getClaudeConfigDir`, `getUserConfigPath`, `getProjectConfigPath`, `getDataDir` | Features, Hooks |
+| Config Management | `deepMerge`, `parseJsonc`, `isHookDisabled`, `configErrors` | index.ts, CLI |
+| Text Processing | `resolveCommandsInText`, `resolveFileReferencesInText`, `parseFrontmatter` | Commands, Rules |
+| Output Control | `dynamicTruncate` | Tools (Grep, LSP) |
+| Normalization | `transformToolName`, `objectToSnakeCase`, `sanitizeModelName` | Hooks, Agents |
+| Compatibility | `migration.ts` | Config loading |
+
+## WHEN TO USE WHAT
+
+| Task | Utility | Notes |
+|------|---------|-------|
+| Find Claude Code configs | `getClaudeConfigDir()` | Never hardcode `~/.claude` |
+| Merge settings (default → user → project) | `deepMerge(base, override)` | Arrays replaced, objects merged |
+| Parse user config files | `parseJsonc()` | Supports comments and trailing commas |
+| Check if hook should run | `isHookDisabled(name, disabledHooks)` | Respects `disabled_hooks` config |
+| Truncate large tool output | `dynamicTruncate(text, budget, reserved)` | Token-aware, prevents overflow |
+| Resolve `@file` references | `resolveFileReferencesInText()` | maxDepth=3 prevents infinite loops |
+| Execute shell commands | `resolveCommandsInText()` | Supports `!`\`command\`\` syntax |
+| Handle legacy agent names | `migrateLegacyAgentNames()` | `omo` → `Sisyphus` |
+
+## CRITICAL PATTERNS
+
+### Dynamic Truncation
+```typescript
+import { dynamicTruncate } from "../shared"
+// Keep 50% headroom, max 50k tokens
+const output = dynamicTruncate(result, remainingTokens, 0.5)
+```
+
+### Deep Merge Priority
+```typescript
+const final = deepMerge(defaults, userConfig)
+final = deepMerge(final, projectConfig) // Project wins
+```
+
+### Safe JSONC Parsing
+```typescript
+const { config, error } = parseJsoncSafe(content)
+if (error) return fallback
+```
+
+## ANTI-PATTERNS (SHARED)
+
+- **Hardcoding paths**: Use `getClaudeConfigDir()`, `getUserConfigPath()`
+- **Manual JSON.parse**: Use `parseJsonc()` for user files (comments allowed)
+- **Ignoring truncation**: Large outputs MUST use `dynamicTruncate`
+- **Direct string concat for configs**: Use `deepMerge` for proper priority