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/atlas/git-diff-stats.ts

@@ -0,0 +1,108 @@
+import { execSync } from "node:child_process"
+
+interface GitFileStat {
+  path: string
+  added: number
+  removed: number
+  status: "modified" | "added" | "deleted"
+}
+
+export function getGitDiffStats(directory: string): GitFileStat[] {
+  try {
+    const output = execSync("git diff --numstat HEAD", {
+      cwd: directory,
+      encoding: "utf-8",
+      timeout: 5000,
+      stdio: ["pipe", "pipe", "pipe"],
+    }).trim()
+
+    if (!output) return []
+
+    const statusOutput = execSync("git status --porcelain", {
+      cwd: directory,
+      encoding: "utf-8",
+      timeout: 5000,
+      stdio: ["pipe", "pipe", "pipe"],
+    }).trim()
+
+    const statusMap = new Map<string, "modified" | "added" | "deleted">()
+    for (const line of statusOutput.split("\n")) {
+      if (!line) continue
+      const status = line.substring(0, 2).trim()
+      const filePath = line.substring(3)
+      if (status === "A" || status === "??") {
+        statusMap.set(filePath, "added")
+      } else if (status === "D") {
+        statusMap.set(filePath, "deleted")
+      } else {
+        statusMap.set(filePath, "modified")
+      }
+    }
+
+    const stats: GitFileStat[] = []
+    for (const line of output.split("\n")) {
+      const parts = line.split("\t")
+      if (parts.length < 3) continue
+
+      const [addedStr, removedStr, path] = parts
+      const added = addedStr === "-" ? 0 : parseInt(addedStr, 10)
+      const removed = removedStr === "-" ? 0 : parseInt(removedStr, 10)
+
+      stats.push({
+        path,
+        added,
+        removed,
+        status: statusMap.get(path) ?? "modified",
+      })
+    }
+
+    return stats
+  } catch {
+    return []
+  }
+}
+
+export function formatFileChanges(stats: GitFileStat[], notepadPath?: string): string {
+  if (stats.length === 0) return "[FILE CHANGES SUMMARY]\nNo file changes detected.\n"
+
+  const modified = stats.filter((s) => s.status === "modified")
+  const added = stats.filter((s) => s.status === "added")
+  const deleted = stats.filter((s) => s.status === "deleted")
+
+  const lines: string[] = ["[FILE CHANGES SUMMARY]"]
+
+  if (modified.length > 0) {
+    lines.push("Modified files:")
+    for (const f of modified) {
+      lines.push(`  ${f.path}  (+${f.added}, -${f.removed})`)
+    }
+    lines.push("")
+  }
+
+  if (added.length > 0) {
+    lines.push("Created files:")
+    for (const f of added) {
+      lines.push(`  ${f.path}  (+${f.added})`)
+    }
+    lines.push("")
+  }
+
+  if (deleted.length > 0) {
+    lines.push("Deleted files:")
+    for (const f of deleted) {
+      lines.push(`  ${f.path}  (-${f.removed})`)
+    }
+    lines.push("")
+  }
+
+  if (notepadPath) {
+    const notepadStat = stats.find((s) => s.path.includes("notepad") || s.path.includes(".sisyphus"))
+    if (notepadStat) {
+      lines.push("[NOTEPAD UPDATED]")
+      lines.push(`  ${notepadStat.path}  (+${notepadStat.added})`)
+      lines.push("")
+    }
+  }
+
+  return lines.join("\n")
+}