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/_source/pi/SKILL.md

@@ -0,0 +1,99 @@
+---
+name: atlassian
+description: Interact with Atlassian Cloud Jira and Confluence through a portable task-oriented CLI for search, issue/page edits, comments, transitions, and bounded raw requests.
+---
+
+# Atlassian (Pi)
+
+Portable Atlassian workflows for pi using the shared TypeScript CLI in `scripts/`.
+
+## Requirements
+
+- Node.js 20+
+- `pnpm`
+- Atlassian Cloud account access
+- `ATLASSIAN_BASE_URL`
+- `ATLASSIAN_EMAIL`
+- `ATLASSIAN_API_TOKEN`
+
+The `ATLASSIAN_*` values may come from the shell environment or a `.env` file in the installed skill's `scripts/` directory.
+
+## First-Time Setup
+
+Global install:
+
+```bash
+mkdir -p ~/.pi/agent/skills/atlassian
+cp -R skills/atlassian/pi/* ~/.pi/agent/skills/atlassian/
+cd ~/.pi/agent/skills/atlassian/scripts
+pnpm install
+```
+
+Project-local install:
+
+```bash
+mkdir -p .pi/skills/atlassian
+cp -R skills/atlassian/pi/* .pi/skills/atlassian/
+cd .pi/skills/atlassian/scripts
+pnpm install
+```
+
+Pi can also load this repo through settings or package installs as documented in [docs/PI.md](../../../docs/PI.md).
+
+If you installed this repo from a local checkout with `./scripts/install-pi-package.sh`, the runtime stays in the checkout mirror at `pi-package/skills/atlassian/scripts`.
+
+## Prerequisite Check (MANDATORY)
+
+Run inside the skill runtime directory that matches your install style:
+
+- local checkout package install: `pi-package/skills/atlassian/scripts`
+- project-local copied install: `.pi/skills/atlassian/scripts`
+- global copied install: `~/.pi/agent/skills/atlassian/scripts`
+
+```bash
+cd pi-package/skills/atlassian/scripts
+node -e "require.resolve('commander');require.resolve('dotenv');console.log('OK: runtime dependencies installed')"
+node -e 'require("dotenv").config({ path: ".env" }); const required = ["ATLASSIAN_BASE_URL", "ATLASSIAN_EMAIL", "ATLASSIAN_API_TOKEN"]; const missing = required.filter((key) => !(process.env[key] || "").trim()); if (missing.length) { console.error("Missing required Atlassian config: " + missing.join(", ")); process.exit(1); } console.log("OK: Atlassian config present")'
+pnpm atlassian health
+```
+
+If any check fails, stop and return:
+
+`Missing dependency/config: atlassian requires installed CLI dependencies and valid Atlassian Cloud credentials. Configure ATLASSIAN_* in the shell environment or scripts/.env, then retry.`
+
+## Supported Commands
+
+- `pnpm atlassian health`
+- `pnpm atlassian jira-search --jql "..."`
+- `pnpm atlassian jira-get --issue ABC-123`
+- `pnpm atlassian jira-create ... [--dry-run]`
+- `pnpm atlassian jira-update ... [--dry-run]`
+- `pnpm atlassian jira-comment ... [--dry-run]`
+- `pnpm atlassian jira-transitions --issue ABC-123`
+- `pnpm atlassian jira-transition ... [--dry-run]`
+- `pnpm atlassian conf-search --query "..."`
+- `pnpm atlassian conf-get --page 12345`
+- `pnpm atlassian conf-create ... [--dry-run]`
+- `pnpm atlassian conf-update ... [--dry-run]`
+- `pnpm atlassian conf-comment ... [--dry-run]`
+- `pnpm atlassian conf-children --page 12345`
+- `pnpm atlassian raw --product jira|confluence --method GET|POST|PUT --path ...`
+
+## Usage Examples
+
+- `pnpm atlassian jira-search --jql "project = ENG ORDER BY updated DESC" --max-results 10`
+- `pnpm atlassian conf-comment --page 12345 --body-file comment.storage.html --dry-run`
+- `pnpm atlassian raw --product jira --method GET --path "/rest/api/3/issue/ENG-123"`
+
+## Safety Rules
+
+- Default output is JSON; prefer that for agent workflows.
+- Use `--dry-run` before any mutating command unless the user clearly wants the write to happen immediately.
+- `raw` is for explicit edge cases only and does not allow `DELETE`.
+- `--body-file` must stay inside the current workspace.
+- Confluence write bodies should be storage-format inputs in v1.
+
+## Notes
+
+- Atlassian Cloud is the primary supported platform in v1.
+- Package installs use the repo's `pi-package/skills/atlassian/` mirror so the installed skill directory name matches `atlassian`.