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

docs/PI-RESEARCH.md

@@ -2,7 +2,8 @@
 
 ## Scope
 
-This document records the pi-specific findings that drive the `pi` variants in this repo. It is intentionally source-backed so later skill work does not rely on memory or assumptions.
+This document records the pi-specific findings that drive the `pi` variants in this repo. It is
+intentionally source-backed so later skill work does not rely on memory or assumptions.
 
 Checked on `2026-04-23`.
 
@@ -32,11 +33,15 @@ Important discovery details from the skills docs:
 - top-level `.md` files are loaded as skills in pi-native roots like `.pi/skills/`
 - per the upstream skills docs, top-level `.md` files are ignored in `.agents/skills/`
 
-Implication for this repo: `skills/<skill>/pi/SKILL.md` fits pi's recursive discovery model cleanly for source authoring and manual copies, but it is not clean for package-discovered installs because Pi requires the immediate parent directory of `SKILL.md` to match the skill frontmatter `name`.
+Implication for this repo: `skills/<skill>/pi/SKILL.md` fits pi's recursive discovery model
+cleanly for source authoring and manual copies, but it is not clean for package-discovered installs
+because Pi requires the immediate parent directory of `SKILL.md` to match the skill frontmatter
+`name`.
 
 ### Package Support
 
-Pi packages are a first-class distribution path. The package docs say pi can load resources through conventional directories like `skills/`, or through explicit `pi` manifest entries in `package.json`.
+Pi packages are a first-class distribution path. The package docs say pi can load resources through
+conventional directories like `skills/`, or through explicit `pi` manifest entries in `package.json`.
 
 Relevant package behaviors:
 
@@ -46,11 +51,16 @@ Relevant package behaviors:
 - installed pi packages can also ship `extensions/`, `prompts/`, and `themes/`
 - when pi installs npm or git packages, it runs `npm install`
 
-Implication for this repo: a single repo-level `package.json` is a viable v1 surface for shipping only the Pi resources, but the package-facing skill directories must be shaped like `<skill-name>/SKILL.md`. That means the repo should preserve `skills/<family>/pi/` for editing and expose a separate mirror such as `pi-package/skills/<skill-name>/` to Pi.
+Implication for this repo: a single repo-level `package.json` is a viable v1 surface for shipping
+only the Pi resources, but the package-facing skill directories must be shaped like
+`<skill-name>/SKILL.md`. That means the repo should preserve `skills/<family>/pi/` for editing and
+expose a separate mirror such as `pi-package/skills/<skill-name>/` to Pi.
 
 ### Settings And Path Overrides
 
-Pi settings support `packages`, `extensions`, `skills`, `prompts`, and `themes`. In both `~/.pi/agent/settings.json` and `.pi/settings.json`, the `skills` array can point to local files or directories, and the docs explicitly allow absolute paths and `~`.
+Pi settings support `packages`, `extensions`, `skills`, `prompts`, and `themes`. In both
+`~/.pi/agent/settings.json` and `.pi/settings.json`, the `skills` array can point to local files
+or directories, and the docs explicitly allow absolute paths and `~`.
 
 Implication for this repo:
 
@@ -68,18 +78,23 @@ Pi extensions are TypeScript modules that can:
 - add UI interactions and custom components
 - persist session state
 
-The coding-agent README explicitly lists advanced behaviors like sub-agents, plan mode, permission gates, MCP integration, and git checkpointing as extension-capable areas.
+The coding-agent README explicitly lists advanced behaviors like sub-agents, plan mode, permission
+gates, MCP integration, and git checkpointing as extension-capable areas.
 
-Implication for this repo: extensions are a real opportunity for workflow-heavy skills, but they are optional for the initial skill port. The base skill variants should remain usable without any extension dependency.
+Implication for this repo: extensions are a real opportunity for workflow-heavy skills, but they
+are optional for the initial skill port. The base skill variants should remain usable without any
+extension dependency.
 
 ### Cross-Harness Compatibility
 
-The pi skills docs explicitly call out `~/.agents/skills/` as a supported global skill root, and describe adding Codex or Claude skill directories through settings when needed.
+The pi skills docs explicitly call out `~/.agents/skills/` as a supported global skill root, and
+describe adding Codex or Claude skill directories through settings when needed.
 
 Implication for this repo:
 
 - existing Superpowers installs exposed through `~/.agents/skills/` can already be visible to pi
-- pi-specific skill variants still need their own instructions because pi does not share Codex's `update_plan`, plan-mode, or worktree assumptions
+- pi-specific skill variants still need their own instructions because pi does not share Codex's
+  `update_plan`, plan-mode, or worktree assumptions
 
 ## Decisions Derived From Research