feat(M4): Reusable code abstractions and dead-code removal

scripts/generate-skills.mjs

@@ -487,8 +487,12 @@ async function generateReviewerRuntimePi(repoRoot, writeRoot) {
 
 /**
  * Clear generated content in a root, preserving:
- *   - node_modules (installed by pnpm)
+ *   - node_modules (installed by pnpm) — at any depth
  *   - .generated-manifest.json (will be rewritten after generation)
+ *
+ * Subdirectories are always recursed into before removal so that
+ * node_modules trees nested at any depth (e.g. scripts/node_modules inside
+ * atlassian or web-automation variants) are preserved.
  */
 async function clearGeneratedRoot(rootDir) {
   let entries;
@@ -501,7 +505,18 @@ async function clearGeneratedRoot(rootDir) {
   for (const entry of entries) {
     if (entry.name === "node_modules") continue;
     if (entry.name === MANIFEST_FILENAME) continue;
-    await rm(path.join(rootDir, entry.name), { recursive: true, force: true });
+    const fullPath = path.join(rootDir, entry.name);
+    if (entry.isDirectory()) {
+      // Always recurse so node_modules at any depth is preserved.
+      await clearGeneratedRoot(fullPath);
+      // Remove the directory only if nothing protected remains inside it.
+      const remaining = await readdir(fullPath).catch(() => []);
+      if (remaining.length === 0) {
+        await rm(fullPath, { force: true });
+      }
+    } else {
+      await rm(fullPath, { force: true });
+    }
   }
 }
 
@@ -521,6 +536,7 @@ const SCRIPTS_SKILL_CONFIGS = {
       "check-install.js",
       "extract.js",
       "flow.ts",
+      "lib",
       "scan-local-app.ts",
       "scrape.ts",
       "test-full.ts",