Refresh configs, add update.fish, rewrite README as setup runbook

- Re-dump brewfile (adds postgresql@16, tree; drops typeit4me)
- Refresh claude-settings.json, hosts, and serena_config.yml from machine
- Add update.fish to actualise the copied configs in one go
- Rewrite README as a complete ordered fresh-machine setup guide

Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01MN5eka2MuNJP9uCMdTda75

brewfile

@@ -1,61 +1,144 @@
+# Official Amazon AWS command-line interface
 brew "awscli"
+# Azure Storage data transfer utility
+brew "azcopy"
+# Clone of cat(1) with syntax highlighting and Git integration
 brew "bat"
+# Play, record, convert, and stream select audio and video codecs
+brew "ffmpeg"
+# User-friendly command-line shell for UNIX-like operating systems
 brew "fish"
+# Command-line fuzzy finder written in Go
 brew "fzf"
+# GitHub command-line tool
 brew "gh"
+# CLI for Drive, Gmail, Calendar, Sheets, Docs, Chat, Admin, and more
+brew "googleworkspace-cli"
+# Open-source build automation tool based on the Groovy and Kotlin DSL
+brew "gradle"
+# CLI for Infisical
 brew "infisical"
+# Postgres C API library
 brew "libpq"
+# Open-source, cross-platform JavaScript runtime environment
 brew "node"
+# Development kit for the Java programming language
+brew "openjdk@17"
+# Development kit for the Java programming language
+brew "openjdk@21"
+# Drop-in replacement for Terraform. Infrastructure as Code Tool
 brew "opentofu"
+# Fast, disk space efficient package manager
 brew "pnpm"
+# PDF rendering library (based on the xpdf-3.0 code base)
+brew "poppler"
+# Object-relational database system
+brew "postgresql@16", link: true
+# Cross-shell prompt for astronauts
 brew "starship"
+# SMTP command-line test tool
 brew "swaks"
+# Terminal multiplexer
 brew "tmux"
+# Display directories as trees (with optional color/HTML output)
+brew "tree"
+# Extremely fast Python package installer and resolver, written in Rust
 brew "uv"
+# Library to create, extract, and modify Windows Imaging files
+brew "wimlib"
+# Feature-rich command-line audio/video downloader
+brew "yt-dlp"
+# Password manager that keeps all passwords secure behind one password
 cask "1password"
+# Command-line interface for 1Password
+cask "1password-cli"
+# Application launcher and productivity software
 cask "alfred"
+# Command-line tools for building and debugging Android apps
+cask "android-commandlinetools"
+# Integrated CAD, CAM, CAE, and PCB software
+cask "autodesk-fusion"
+# Menu bar icon organiser
 cask "bartender"
+# Tool to customise input devices and automate computer systems
 cask "bettertouchtool"
+# Web debugging Proxy application
 cask "charles"
+# Anthropic's official Claude AI desktop app
 cask "claude"
+# Terminal-based AI coding assistant
 cask "claude-code"
+# Tool to remove unnecessary files and folders from disk
 cask "cleanmymac"
+# Screen capturing tool
 cask "cleanshot"
+# Customise mouse movements between multiple displays
 cask "cursr"
+# Drivers for DisplayLink docks, adapters and monitors
 cask "displaylink"
+# App to build and share containerised applications and microservices
 cask "docker-desktop"
 cask "font-fira-code-nerd-font"
+# GIT client
 cask "fork"
+# Finder replacement and FTP, SFTP, WebDAV and Amazon s3 client
 cask "forklift"
+# Kubernetes IDE
 cask "freelens"
+# Free and open-source image editor
 cask "gimp"
+# Web browser
 cask "google-chrome"
+# Client for the Google Drive storage service
 cask "google-drive"
+# Companion app for Home Assistant home automation software
 cask "home-assistant"
 cask "insomnium"
+# Terminal emulator as alternative to Apple's Terminal app
 cask "iterm2"
+# JetBrains tools manager
 cask "jetbrains-toolbox"
+# Explorer for Azure Storage
 cask "microsoft-azure-storage-explorer"
+# Smooths scrolling and set mouse scroll directions independently
 cask "mos"
+# Reverse proxy, secure introspectable tunnels to localhost
+cask "ngrok"
+# Knowledge base that works on top of a local folder of plain text Markdown files
 cask "obsidian"
+# Finder Toolbar app to open the current directory in Terminal or Editor
 cask "openinterminal"
+# RAW photo processor
+cask "rawtherapee"
+# Email client
 cask "readdle-spark"
+# Team communication and collaboration software
 cask "slack"
+# Music streaming service
 cask "spotify"
+# Messaging app with a focus on speed and security
 cask "telegram"
+# Unpacks archive files
 cask "the-unarchiver"
+# To-do list
 cask "todoist-app"
-cask "typeit4me"
+# PDF editor
 cask "updf"
+# Open-source code editor
 cask "visual-studio-code"
+# Native desktop client for WhatsApp
 cask "whatsapp"
+# Connect to Windows
 cask "windows-app"
+# Gecko based web browser
 cask "zen"
 vscode "alefragnani.project-manager"
 vscode "anthropic.claude-code"
 vscode "astro-build.astro-vscode"
 vscode "dbaeumer.vscode-eslint"
 vscode "dracula-theme.theme-dracula"
+vscode "fwcd.kotlin"
+vscode "github.vscode-github-actions"
 vscode "hashicorp.terraform"
 vscode "ms-python.debugpy"
 vscode "ms-python.python"
@@ -63,5 +146,6 @@ vscode "ms-python.vscode-pylance"
 vscode "ms-python.vscode-python-envs"
 vscode "pkief.material-icon-theme"
 vscode "redhat.vscode-yaml"
+vscode "tomoki1207.pdf"
 vscode "usernamehw.errorlens"
 vscode "vue.volar"