Perform code optimization and document cleanup (#1)

## Summary
- add repository-wide quality tooling and verification scaffolding, including CI workflows, pnpm workspace setup, ESLint/Prettier/markdown checks, and generated-output verification helpers
- reorganize skill sources and generation flow by introducing canonical `_source` variants, generator/manifests, reusable helper abstractions, and shared web-automation/browser utilities
- clean up and expand documentation so the root README flows into docs and skill docs, with clearer development, reviewer, installer, and workflow guidance

## Notable changes
- docs flow and consistency cleanup across `README.md`, `docs/README.md`, and related docs
- new scripts for `check`, docs verification, generated-file verification, shell portability, and safe directory replacement
- refactors in Atlassian and web-automation skill runtimes to reduce duplication and centralize reusable code
- changelog, development documentation, and CI surface updates

## Test Plan
- [ ] `pnpm run check`
- [ ] review generated/manifests and skill sync outputs
- [ ] smoke-check docs flow from `README.md` to `docs/README.md` to skill docs

## Notes
- this branch currently includes tracked `skills/web-automation/shared/node_modules` content that should be reviewed carefully as potentially noisy/accidental committed artifacts

Co-authored-by: Stefano Fiorini <stefano.fiorini@firsthorizon.com>
Reviewed-on: #1

scripts/lib/skill-manager-core.mjs

@@ -279,7 +279,7 @@ async function findClaudeCodeSuperpowersPluginRoots(homeDir) {
 
 async function findCursorSuperpowersPluginRoots(homeDir) {
   const pluginRoot = path.join(homeDir, ".cursor", "plugins", "cache", "cursor-public", "superpowers");
-  let entries = [];
+  let entries;
   try {
     entries = await readdir(pluginRoot, { withFileTypes: true });
   } catch (error) {
@@ -532,6 +532,24 @@ export async function buildOperationPlan({ selections, repoRoot = process.cwd(),
   return { operations, prompts, reportRows, assumeYes };
 }
 
+/**
+ * Remove the target of an operation (skill, helper, or superpowers).
+ *
+ * Validates that the target is within the skills root before removing.
+ * Handles both regular directories and symbolic links.
+ * Idempotent: succeeds even when the target does not exist.
+ *
+ * @param {object} op - Operation object with at least `target` and `skillsRoot`.
+ * @returns {Promise<object>} Operation with `status: "ok"`.
+ */
+export async function removeTarget(op) {
+  await validateRemoveTarget(op.target, op.skillsRoot, { repoRoot: REPO_ROOT });
+  const info = existsSync(op.target) ? await lstat(op.target) : null;
+  if (info?.isSymbolicLink()) await unlink(op.target);
+  else await rm(op.target, { recursive: true, force: true });
+  return { ...op, status: "ok" };
+}
+
 export async function validateRemoveTarget(target, skillsRoot, { repoRoot = process.cwd() } = {}) {
   const resolvedRoot = path.resolve(skillsRoot);
   const resolvedTarget = path.resolve(target);
@@ -598,7 +616,8 @@ export async function executeOperation(op) {
   if (op.action === "unsupported" || op.status === "skipped") return { ...op, status: "skipped" };
   if (op.kind === "package-skill") return { ...op, status: "included" };
   if (op.kind === "sync-pi-package") {
-    runCommand(path.join(op.repoRoot, "scripts", "sync-pi-package-skills.sh"), [], { cwd: op.repoRoot });
+    // Use the canonical generator (pnpm run sync:pi / node scripts/generate-skills.mjs).
+    runCommand(process.execPath, [path.join(op.repoRoot, "scripts", "generate-skills.mjs")], { cwd: op.repoRoot });
     return { ...op, status: "ok" };
   }
   if (op.kind === "pi-package") {
@@ -607,33 +626,19 @@ export async function executeOperation(op) {
     return { ...op, status: "ok" };
   }
   if (op.kind === "skill") {
-    if (op.action === "remove") {
-      await validateRemoveTarget(op.target, op.skillsRoot, { repoRoot: REPO_ROOT });
-      const info = existsSync(op.target) ? await lstat(op.target) : null;
-      if (info?.isSymbolicLink()) await unlink(op.target);
-      else await rm(op.target, { recursive: true, force: true });
-      return { ...op, status: "ok" };
-    }
+    if (op.action === "remove") return removeTarget(op);
     await copyDirectoryReplacing(op.source, op.target);
     return { ...op, status: "ok" };
   }
   if (op.kind === "helper") {
-    if (op.action === "remove") {
-      await validateRemoveTarget(op.target, op.skillsRoot, { repoRoot: REPO_ROOT });
-      const info = existsSync(op.target) ? await lstat(op.target) : null;
-      if (info?.isSymbolicLink()) await unlink(op.target);
-      else await rm(op.target, { recursive: true, force: true });
-      return { ...op, status: "ok" };
-    }
+    if (op.action === "remove") return removeTarget(op);
     await installHelperAllowlist(op);
     return { ...op, status: "ok" };
   }
   if (op.kind === "superpowers") {
+    if (op.action === "remove") return removeTarget(op);
     await mkdir(path.dirname(op.target), { recursive: true });
-    if (op.action === "remove") {
-      await validateRemoveTarget(op.target, op.skillsRoot, { repoRoot: REPO_ROOT });
-      await rm(op.target, { recursive: true, force: true });
-    } else if (op.mode === "copy") {
+    if (op.mode === "copy") {
       await copyDirectoryReplacing(op.source, op.target);
     } else {
       await rm(op.target, { recursive: true, force: true });