refactor: wave 1 - extract leaf modules, rename catch-all files, split index.ts hooks

- Split 25+ index.ts files into hook.ts + extracted modules
- Rename all catch-all utils.ts/helpers.ts to domain-specific names
- Split src/tools/lsp/ into ~15 focused modules
- Split src/tools/delegate-task/ into ~18 focused modules
- Separate shared types from implementation
- 155 files changed, 60+ new files created
- All typecheck clean, 61 tests pass

src/agents/atlas/prompt-section-builder.ts

@@ -0,0 +1,138 @@
+/**
+ * Atlas Orchestrator - Shared Utilities
+ *
+ * Common functions for building dynamic prompt sections used by both
+ * default (Claude-optimized) and GPT-optimized prompts.
+ */
+
+import type { CategoryConfig } from "../../config/schema"
+import { formatCustomSkillsBlock, type AvailableAgent, type AvailableSkill } from "../dynamic-agent-prompt-builder"
+import { DEFAULT_CATEGORIES, CATEGORY_DESCRIPTIONS } from "../../tools/delegate-task/constants"
+import { truncateDescription } from "../../shared/truncate-description"
+
+export const getCategoryDescription = (name: string, userCategories?: Record<string, CategoryConfig>) =>
+  userCategories?.[name]?.description ?? CATEGORY_DESCRIPTIONS[name] ?? "General tasks"
+
+export function buildAgentSelectionSection(agents: AvailableAgent[]): string {
+   if (agents.length === 0) {
+     return `##### Option B: Use AGENT directly (for specialized experts)
+
+ No agents available.`
+   }
+
+   const rows = agents.map((a) => {
+     const shortDesc = truncateDescription(a.description)
+     return `| \`${a.name}\` | ${shortDesc} |`
+   })
+
+  return `##### Option B: Use AGENT directly (for specialized experts)
+
+| Agent | Best For |
+|-------|----------|
+${rows.join("\n")}`
+}
+
+export function buildCategorySection(userCategories?: Record<string, CategoryConfig>): string {
+  const allCategories = { ...DEFAULT_CATEGORIES, ...userCategories }
+  const categoryRows = Object.entries(allCategories).map(([name, config]) => {
+    const temp = config.temperature ?? 0.5
+    return `| \`${name}\` | ${temp} | ${getCategoryDescription(name, userCategories)} |`
+  })
+
+  return `##### Option A: Use CATEGORY (for domain-specific work)
+
+Categories spawn \`Sisyphus-Junior-{category}\` with optimized settings:
+
+| Category | Temperature | Best For |
+|----------|-------------|----------|
+${categoryRows.join("\n")}
+
+\`\`\`typescript
+task(category="[category-name]", load_skills=[...], run_in_background=false, prompt="...")
+\`\`\``
+}
+
+export function buildSkillsSection(skills: AvailableSkill[]): string {
+  if (skills.length === 0) {
+    return ""
+  }
+
+  const builtinSkills = skills.filter((s) => s.location === "plugin")
+  const customSkills = skills.filter((s) => s.location !== "plugin")
+
+   const builtinRows = builtinSkills.map((s) => {
+     const shortDesc = truncateDescription(s.description)
+     return `| \`${s.name}\` | ${shortDesc} |`
+   })
+
+   const customRows = customSkills.map((s) => {
+     const shortDesc = truncateDescription(s.description)
+     const source = s.location === "project" ? "project" : "user"
+     return `| \`${s.name}\` | ${shortDesc} | ${source} |`
+   })
+
+  const customSkillBlock = formatCustomSkillsBlock(customRows, customSkills, "**")
+
+  let skillsTable: string
+
+  if (customSkills.length > 0 && builtinSkills.length > 0) {
+    skillsTable = `**Built-in Skills:**
+
+| Skill | When to Use |
+|-------|-------------|
+${builtinRows.join("\n")}
+
+${customSkillBlock}`
+  } else if (customSkills.length > 0) {
+    skillsTable = customSkillBlock
+  } else {
+    skillsTable = `| Skill | When to Use |
+|-------|-------------|
+${builtinRows.join("\n")}`
+  }
+
+  return `
+#### 3.2.2: Skill Selection (PREPEND TO PROMPT)
+
+**Skills are specialized instructions that guide subagent behavior. Consider them alongside category selection.**
+
+${skillsTable}
+
+**MANDATORY: Evaluate ALL skills (built-in AND user-installed) for relevance to your task.**
+
+Read each skill's description and ask: "Does this skill's domain overlap with my task?"
+- If YES: INCLUDE in load_skills=[...]
+- If NO: You MUST justify why in your pre-delegation declaration
+
+**Usage:**
+\`\`\`typescript
+task(category="[category]", load_skills=["skill-1", "skill-2"], run_in_background=false, prompt="...")
+\`\`\`
+
+**IMPORTANT:**
+- Skills get prepended to the subagent's prompt, providing domain-specific instructions
+- Subagents are STATELESS - they don't know what skills exist unless you include them
+- Missing a relevant skill = suboptimal output quality`
+}
+
+export function buildDecisionMatrix(agents: AvailableAgent[], userCategories?: Record<string, CategoryConfig>): string {
+  const allCategories = { ...DEFAULT_CATEGORIES, ...userCategories }
+
+  const categoryRows = Object.entries(allCategories).map(([name]) =>
+    `| ${getCategoryDescription(name, userCategories)} | \`category="${name}", load_skills=[...]\` |`
+  )
+
+   const agentRows = agents.map((a) => {
+     const shortDesc = truncateDescription(a.description)
+     return `| ${shortDesc} | \`agent="${a.name}"\` |`
+   })
+
+  return `##### Decision Matrix
+
+| Task Domain | Use |
+|-------------|-----|
+${categoryRows.join("\n")}
+${agentRows.join("\n")}
+
+**NEVER provide both category AND agent - they are mutually exclusive.**`
+}