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/builtin-agents/atlas-agent.ts

@@ -0,0 +1,63 @@
+import type { AgentConfig } from "@opencode-ai/sdk"
+import type { AgentOverrides } from "../types"
+import type { CategoriesConfig, CategoryConfig } from "../../config/schema"
+import type { AvailableAgent, AvailableSkill } from "../dynamic-agent-prompt-builder"
+import { AGENT_MODEL_REQUIREMENTS } from "../../shared"
+import { applyOverrides } from "./agent-overrides"
+import { applyModelResolution } from "./model-resolution"
+import { createAtlasAgent } from "../atlas"
+
+export function maybeCreateAtlasConfig(input: {
+  disabledAgents: string[]
+  agentOverrides: AgentOverrides
+  uiSelectedModel?: string
+  availableModels: Set<string>
+  systemDefaultModel?: string
+  availableAgents: AvailableAgent[]
+  availableSkills: AvailableSkill[]
+  mergedCategories: Record<string, CategoryConfig>
+  userCategories?: CategoriesConfig
+}): AgentConfig | undefined {
+  const {
+    disabledAgents,
+    agentOverrides,
+    uiSelectedModel,
+    availableModels,
+    systemDefaultModel,
+    availableAgents,
+    availableSkills,
+    mergedCategories,
+    userCategories,
+  } = input
+
+  if (disabledAgents.includes("atlas")) return undefined
+
+  const orchestratorOverride = agentOverrides["atlas"]
+  const atlasRequirement = AGENT_MODEL_REQUIREMENTS["atlas"]
+
+  const atlasResolution = applyModelResolution({
+    uiSelectedModel: orchestratorOverride?.model ? undefined : uiSelectedModel,
+    userModel: orchestratorOverride?.model,
+    requirement: atlasRequirement,
+    availableModels,
+    systemDefaultModel,
+  })
+
+  if (!atlasResolution) return undefined
+  const { model: atlasModel, variant: atlasResolvedVariant } = atlasResolution
+
+  let orchestratorConfig = createAtlasAgent({
+    model: atlasModel,
+    availableAgents,
+    availableSkills,
+    userCategories,
+  })
+
+  if (atlasResolvedVariant) {
+    orchestratorConfig = { ...orchestratorConfig, variant: atlasResolvedVariant }
+  }
+
+  orchestratorConfig = applyOverrides(orchestratorConfig, orchestratorOverride, mergedCategories)
+
+  return orchestratorConfig
+}