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/create-plan/pi/.generated-manifest.json

@@ -0,0 +1,31 @@
+{
+  "$schema": "https://ai-coding-skills.dev/schemas/generated-manifest/v1.json",
+  "generator": "scripts/generate-skills.mjs",
+  "generatedRoot": "skills/create-plan/pi",
+  "files": [
+    {
+      "path": "SKILL.md",
+      "kind": "file",
+      "mode": "644",
+      "sha256": "8767db25ce6f03e141ce4c48f37e9d7c4958c3cf3d70729f3bd7214b84f6d065"
+    },
+    {
+      "path": "templates/continuation-runbook.md",
+      "kind": "file",
+      "mode": "644",
+      "sha256": "1685cded3d4abaf03122a490175ff03b7da593ce60cbca97ae15fadcb706617f"
+    },
+    {
+      "path": "templates/milestone-plan.md",
+      "kind": "file",
+      "mode": "644",
+      "sha256": "364c08bf0a5ee3738195a0770db72c5a4c9ad7f7fb89eaa064eb8c67f47ad69a"
+    },
+    {
+      "path": "templates/story-tracker.md",
+      "kind": "file",
+      "mode": "644",
+      "sha256": "ecb550ea9dcd9dde6c813e90af9f538bf5a247fc249e8e323f2b7bf583e52196"
+    }
+  ]
+}

skills/create-plan/pi/SKILL.md

@@ -3,6 +3,8 @@ name: create-plan
 description: Use when a user asks to create or maintain a structured implementation plan in pi, including milestones, bite-sized stories, and resumable local planning artifacts under ai_plan.
 ---
 
+<!-- ⚠️ GENERATED FILE – do not edit directly. Edit the canonical source in skills/create-plan/_source/pi/ and run `pnpm run sync:pi`. -->
+
 # Create Plan (Pi)
 
 Create and maintain a local plan workspace under `ai_plan/` at project root.

skills/create-plan/pi/templates/continuation-runbook.md

@@ -1,3 +1,4 @@
+<!-- ⚠️ GENERATED FILE – do not edit directly. Edit the canonical source in skills/create-plan/_source/pi/ and run `pnpm run sync:pi`. -->
 # Continuation Runbook: [Plan Title]
 
 ## Reference Files (START HERE)
@@ -65,15 +66,19 @@ Work from this folder (`ai_plan/YYYY-MM-DD-<short-title>/`) and always follow th
 ## Full Context Reproduction
 
 ### Project Overview
+
 [What this project/feature is about]
 
 ### User Requirements
+
 [All gathered requirements]
 
 ### Scope
+
 [In scope / out of scope]
 
 ### Dependencies
+
 [External dependencies, prerequisites, related systems]
 
 ---
@@ -81,16 +86,19 @@ Work from this folder (`ai_plan/YYYY-MM-DD-<short-title>/`) and always follow th
 ## Key Specifications
 
 ### Type Definitions
+
 ```typescript
 // Copy-paste ready type definitions
 ```
 
 ### Enums & Constants
+
 ```typescript
 // All enums/constants needed
 ```
 
 ### API Endpoints
+
 ```typescript
 // Request/response shapes
 ```
@@ -108,16 +116,19 @@ Work from this folder (`ai_plan/YYYY-MM-DD-<short-title>/`) and always follow th
 ## Verification Commands
 
 ### Lint (changed files first)
+
 ```bash
 # example: pnpm eslint <changed-file-1> <changed-file-2>
 ```
 
 ### Typecheck
+
 ```bash
 # example: pnpm tsc --noEmit
 ```
 
 ### Tests (target changed scope first)
+
 ```bash
 # example: pnpm test -- <related spec/file>
 ```

skills/create-plan/pi/templates/milestone-plan.md

@@ -1,6 +1,8 @@
+<!-- ⚠️ GENERATED FILE – do not edit directly. Edit the canonical source in skills/create-plan/_source/pi/ and run `pnpm run sync:pi`. -->
 # [Plan Title]
 
 ## Overview
+
 - **Goal:** [One sentence describing the end state]
 - **Created:** YYYY-MM-DD
 - **Status:** In Progress | Complete
@@ -8,37 +10,46 @@
 ## Context
 
 ### Requirements
+
 [Gathered requirements from user questions]
 
 ### Constraints
+
 [Technical, business, or timeline constraints]
 
 ### Success Criteria
+
 [How we know this is complete]
 
 ## Architecture
 
 ### Design Decisions
+
 [Key architectural choices and rationale]
 
 ### Component Relationships
+
 [How pieces fit together]
 
 ### Data Flow
+
 [How data moves through the system]
 
 ## Milestones
 
 ### M1: [Name]
+
 **Description:** [What this milestone achieves]
 
 **Acceptance Criteria:**
+
 - [ ] [Criterion 1]
 - [ ] [Criterion 2]
 
 **Stories:** S-101, S-102, S-103...
 
 **Milestone Completion Rule (MANDATORY):**
+
 - Run lint/typecheck/tests for changed files.
 - Commit locally (DO NOT push).
 - Stop and ask user for feedback.
@@ -48,15 +59,18 @@
 ---
 
 ### M2: [Name]
+
 **Description:** [What this milestone achieves]
 
 **Acceptance Criteria:**
+
 - [ ] [Criterion 1]
 - [ ] [Criterion 2]
 
 **Stories:** S-201, S-202, S-203...
 
 **Milestone Completion Rule (MANDATORY):**
+
 - Run lint/typecheck/tests for changed files.
 - Commit locally (DO NOT push).
 - Stop and ask user for feedback.
@@ -68,16 +82,19 @@
 ## Technical Specifications
 
 ### Types & Interfaces
+
 ```typescript
 // Key type definitions
 ```
 
 ### API Contracts
+
 ```typescript
 // Endpoint signatures, request/response shapes
 ```
 
 ### Constants & Enums
+
 ```typescript
 // Shared constants
 ```
@@ -94,6 +111,7 @@
 ## Related Plan Files
 
 This file is part of the plan folder under `ai_plan/`:
+
 - `original-plan.md` - Original approved plan (reference for original intent)
 - `final-transcript.md` - Final planning transcript (reference for rationale/context)
 - `milestone-plan.md` - This file (full specification)

skills/create-plan/pi/templates/story-tracker.md

@@ -1,6 +1,8 @@
+<!-- ⚠️ GENERATED FILE – do not edit directly. Edit the canonical source in skills/create-plan/_source/pi/ and run `pnpm run sync:pi`. -->
 # Story Tracker: [Plan Title]
 
 ## Progress Summary
+
 - **Current Milestone:** M1
 - **Stories Complete:** 0/N
 - **Milestones Approved:** 0/M
@@ -46,15 +48,18 @@
 ## Update Instructions (MANDATORY)
 
 Before starting any story:
+
 1. Mark story as `in-dev`
 2. Update "Last Updated"
 
 After completing any story:
+
 1. Mark story as `completed`
 2. Add local commit hash to Notes
 3. Update "Stories Complete" and "Last Updated"
 
 At milestone boundary:
+
 1. Run lint/typecheck/tests for changed files
 2. Commit (no push)
 3. Request feedback
@@ -63,4 +68,5 @@ At milestone boundary:
 6. Continue only after approval
 
 After all milestones approved:
+
 - Ask permission to push and then mark plan completed.