docs: update docs for removed packages (opencode, beads)

- Fix broken beads reference in pkgs/default.nix
- Convert opencode.md to deprecation notice with llm-agents.nix link
- Convert beads.md to removal notice
- Remove beads, opencode, openspec from README.md packages table
- Remove beads, opencode from docs/README.md packages list

README.md

@@ -40,7 +40,6 @@ nix run git+https://code.m3ta.dev/m3tam3re/nixpkgs#zellij-ps
 
 | Package            | Description                           |
 | ------------------ | ------------------------------------- |
-| `beads`            | Lightweight memory system for AI coding agents with graph-based issue tracking |
 | `code2prompt`      | Convert code to prompts               |
 | `hyprpaper-random` | Random wallpaper setter for Hyprpaper |
 | `launch-webapp`    | Launch web applications               |
@@ -48,9 +47,7 @@ nix run git+https://code.m3ta.dev/m3tam3re/nixpkgs#zellij-ps
 | `msty-studio`      | Msty Studio application               |
 | `n8n`              | Free and source-available fair-code licensed workflow automation tool |
 | `notesmd-cli`      | Obsidian CLI (Community) - Interact with Obsidian in the terminal |
-| `opencode`         | AI coding agent built for the terminal |
 | `opencode-desktop` | OpenCode Desktop App with Wayland support (includes workaround for upstream issue #11755) |
-| `openspec`         | Spec-driven development (SDD) for AI coding assistants |
 | `pomodoro-timer`   | Pomodoro timer utility                |
 | `rofi-project-opener` | Rofi-based project launcher        |
 | `sidecar`          | Companion tool for CLI agents with diffs, file trees, and task management |