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

docs/README.md

@@ -28,7 +28,6 @@ Step-by-step guides for common tasks:
 
 Documentation for all custom packages:
 
-- [beads](./packages/beads.md) - Lightweight memory system for AI coding agents with graph-based issue tracking
 - [code2prompt](./packages/code2prompt.md) - Convert code to prompts
 - [hyprpaper-random](./packages/hyprpaper-random.md) - Random wallpaper setter for Hyprpaper
 - [launch-webapp](./packages/launch-webapp.md) - Launch web applications
@@ -36,7 +35,6 @@ Documentation for all custom packages:
 - [msty-studio](./packages/msty-studio.md) - Msty Studio application
 - [n8n](./packages/n8n.md) - Free and source-available fair-code licensed workflow automation tool
 - [notesmd-cli](./packages/notesmd-cli.md) - Obsidian CLI (Community) - Interact with Obsidian in the terminal
-- [opencode](./packages/opencode.md) - AI coding agent built for terminal
 - [pomodoro-timer](./packages/pomodoro-timer.md) - Pomodoro timer utility
 - [rofi-project-opener](./packages/rofi-project-opener.md) - Rofi-based project launcher with custom args
 - [sidecar](./packages/sidecar.md) - Companion tool for CLI agents with diffs, file trees, and task management