refactor: wave 2 - split atlas, auto-update-checker, session-recovery, todo-enforcer, background-task hooks

- Extract atlas/ into 15 focused modules (hook, event handler, tool policies, types, etc.)
- Split auto-update-checker into checker/ and hook/ subdirectories with single-purpose files
- Decompose session-recovery into separate recovery strategy files per error type
- Extract todo-continuation-enforcer from monolith to directory with dedicated modules
- Split background-task/tools.ts into individual tool creator files
- Extract command-executor, tmux-utils into focused sub-modules
- Split config/schema.ts into domain-specific schema files
- Decompose cli/config-manager.ts into focused modules
- Rollback skill-mcp-manager, model-availability, index.ts splits that broke tests
- Fix all import path depths for moved files (../../ -> ../../../)
- Add explicit type annotations to resolve TS7006 implicit any errors

Typecheck: 0 errors
Tests: 2359 pass, 5 fail (all pre-existing)

src/hooks/session-recovery/recover-tool-result-missing.ts

@@ -0,0 +1,61 @@
+import type { createOpencodeClient } from "@opencode-ai/sdk"
+import type { MessageData } from "./types"
+import { readParts } from "./storage"
+
+type Client = ReturnType<typeof createOpencodeClient>
+
+interface ToolUsePart {
+  type: "tool_use"
+  id: string
+  name: string
+  input: Record<string, unknown>
+}
+
+interface MessagePart {
+  type: string
+  id?: string
+}
+
+function extractToolUseIds(parts: MessagePart[]): string[] {
+  return parts.filter((part): part is ToolUsePart => part.type === "tool_use" && !!part.id).map((part) => part.id)
+}
+
+export async function recoverToolResultMissing(
+  client: Client,
+  sessionID: string,
+  failedAssistantMsg: MessageData
+): Promise<boolean> {
+  let parts = failedAssistantMsg.parts || []
+  if (parts.length === 0 && failedAssistantMsg.info?.id) {
+    const storedParts = readParts(failedAssistantMsg.info.id)
+    parts = storedParts.map((part) => ({
+      type: part.type === "tool" ? "tool_use" : part.type,
+      id: "callID" in part ? (part as { callID?: string }).callID : part.id,
+    }))
+  }
+
+  const toolUseIds = extractToolUseIds(parts)
+  if (toolUseIds.length === 0) {
+    return false
+  }
+
+  const toolResultParts = toolUseIds.map((id) => ({
+    type: "tool_result" as const,
+    tool_use_id: id,
+    content: "Operation cancelled by user (ESC pressed)",
+  }))
+
+  const promptInput = {
+    path: { id: sessionID },
+    body: { parts: toolResultParts },
+  }
+
+  try {
+    // @ts-expect-error - SDK types may not include tool_result parts
+    await client.session.promptAsync(promptInput)
+
+    return true
+  } catch {
+    return false
+  }
+}