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

skills/atlassian/shared/scripts/src/cli.ts

@@ -3,6 +3,7 @@ import { pathToFileURL } from "node:url";
 
 import { Command } from "commander";
 
+import { resolveFormat } from "./command-helpers.js";
 import { createConfluenceClient } from "./confluence.js";
 import { loadConfig } from "./config.js";
 import { readWorkspaceFile } from "./files.js";
@@ -10,7 +11,7 @@ import { runHealthCheck } from "./health.js";
 import { createJiraClient } from "./jira.js";
 import { writeOutput } from "./output.js";
 import { runRawCommand } from "./raw.js";
-import type { FetchLike, OutputFormat, Writer } from "./types.js";
+import type { FetchLike, Writer } from "./types.js";
 
 type CliContext = {
   cwd?: string;
@@ -20,10 +21,6 @@ type CliContext = {
   stderr?: Writer;
 };
 
-function resolveFormat(format: string | undefined): OutputFormat {
-  return format === "text" ? "text" : "json";
-}
-
 function createRuntime(context: CliContext) {
   const cwd = context.cwd ?? process.cwd();
   const env = context.env ?? process.env;