feat(emacs): Add prebuilt Doom option using nix-doom-emacs-unstraightened

Implement pre-built Doom Emacs packages for the live USB image, eliminating
the need to run `doom sync` after first boot.

Changes:
- Add nix-doom-emacs-unstraightened flake input
- Add homeModule to all three module sets (nixos, unstable, darwin)
- Add `prebuiltDoom` option to emacs role (default: false)
- Enable prebuiltDoom for live-usb configuration
- Pin custom packages in packages.el for deterministic builds:
  - claude-code-ide, gptel-tool-library, beads

When prebuiltDoom=true, all Doom packages are compiled at nix build time
using emacs-overlay. The doom configuration is stored in the nix store
(read-only), and no `doom sync` is required at runtime.

This is ideal for:
- Live USB images
- Immutable/reproducible systems
- Offline deployments

Closes: nixos-configs-1wd

.beads/.gitignore

@@ -0,0 +1,39 @@
+# SQLite databases
+*.db
+*.db?*
+*.db-journal
+*.db-wal
+*.db-shm
+
+# Daemon runtime files
+daemon.lock
+daemon.log
+daemon.pid
+bd.sock
+sync-state.json
+last-touched
+
+# Local version tracking (prevents upgrade notification spam after git ops)
+.local_version
+
+# Legacy database files
+db.sqlite
+bd.db
+
+# Worktree redirect file (contains relative path to main repo's .beads/)
+# Must not be committed as paths would be wrong in other clones
+redirect
+
+# Merge artifacts (temporary files from 3-way merge)
+beads.base.jsonl
+beads.base.meta.json
+beads.left.jsonl
+beads.left.meta.json
+beads.right.jsonl
+beads.right.meta.json
+
+# NOTE: Do NOT add negation patterns (e.g., !issues.jsonl) here.
+# They would override fork protection in .git/info/exclude, allowing
+# contributors to accidentally commit upstream issue databases.
+# The JSONL files (issues.jsonl, interactions.jsonl) and config files
+# are tracked by git by default since no pattern above ignores them.

.beads/README.md

@@ -0,0 +1,81 @@
+# Beads - AI-Native Issue Tracking
+
+Welcome to Beads! This repository uses **Beads** for issue tracking - a modern, AI-native tool designed to live directly in your codebase alongside your code.
+
+## What is Beads?
+
+Beads is issue tracking that lives in your repo, making it perfect for AI coding agents and developers who want their issues close to their code. No web UI required - everything works through the CLI and integrates seamlessly with git.
+
+**Learn more:** [github.com/steveyegge/beads](https://github.com/steveyegge/beads)
+
+## Quick Start
+
+### Essential Commands
+
+```bash
+# Create new issues
+bd create "Add user authentication"
+
+# View all issues
+bd list
+
+# View issue details
+bd show <issue-id>
+
+# Update issue status
+bd update <issue-id> --status in_progress
+bd update <issue-id> --status done
+
+# Sync with git remote
+bd sync
+```
+
+### Working with Issues
+
+Issues in Beads are:
+- **Git-native**: Stored in `.beads/issues.jsonl` and synced like code
+- **AI-friendly**: CLI-first design works perfectly with AI coding agents
+- **Branch-aware**: Issues can follow your branch workflow
+- **Always in sync**: Auto-syncs with your commits
+
+## Why Beads?
+
+✨ **AI-Native Design**
+- Built specifically for AI-assisted development workflows
+- CLI-first interface works seamlessly with AI coding agents
+- No context switching to web UIs
+
+🚀 **Developer Focused**
+- Issues live in your repo, right next to your code
+- Works offline, syncs when you push
+- Fast, lightweight, and stays out of your way
+
+🔧 **Git Integration**
+- Automatic sync with git commits
+- Branch-aware issue tracking
+- Intelligent JSONL merge resolution
+
+## Get Started with Beads
+
+Try Beads in your own projects:
+
+```bash
+# Install Beads
+curl -sSL https://raw.githubusercontent.com/steveyegge/beads/main/scripts/install.sh | bash
+
+# Initialize in your repo
+bd init
+
+# Create your first issue
+bd create "Try out Beads"
+```
+
+## Learn More
+
+- **Documentation**: [github.com/steveyegge/beads/docs](https://github.com/steveyegge/beads/tree/main/docs)
+- **Quick Start Guide**: Run `bd quickstart`
+- **Examples**: [github.com/steveyegge/beads/examples](https://github.com/steveyegge/beads/tree/main/examples)
+
+---
+
+*Beads: Issue tracking that moves at the speed of thought* ⚡

.beads/config.yaml

@@ -0,0 +1,62 @@
+# Beads Configuration File
+# This file configures default behavior for all bd commands in this repository
+# All settings can also be set via environment variables (BD_* prefix)
+# or overridden with command-line flags
+
+# Issue prefix for this repository (used by bd init)
+# If not set, bd init will auto-detect from directory name
+# Example: issue-prefix: "myproject" creates issues like "myproject-1", "myproject-2", etc.
+# issue-prefix: ""
+
+# Use no-db mode: load from JSONL, no SQLite, write back after each command
+# When true, bd will use .beads/issues.jsonl as the source of truth
+# instead of SQLite database
+# no-db: false
+
+# Disable daemon for RPC communication (forces direct database access)
+# no-daemon: false
+
+# Disable auto-flush of database to JSONL after mutations
+# no-auto-flush: false
+
+# Disable auto-import from JSONL when it's newer than database
+# no-auto-import: false
+
+# Enable JSON output by default
+# json: false
+
+# Default actor for audit trails (overridden by BD_ACTOR or --actor)
+# actor: ""
+
+# Path to database (overridden by BEADS_DB or --db)
+# db: ""
+
+# Auto-start daemon if not running (can also use BEADS_AUTO_START_DAEMON)
+# auto-start-daemon: true
+
+# Debounce interval for auto-flush (can also use BEADS_FLUSH_DEBOUNCE)
+# flush-debounce: "5s"
+
+# Git branch for beads commits (bd sync will commit to this branch)
+# IMPORTANT: Set this for team projects so all clones use the same sync branch.
+# This setting persists across clones (unlike database config which is gitignored).
+# Can also use BEADS_SYNC_BRANCH env var for local override.
+# If not set, bd sync will require you to run 'bd config set sync.branch <branch>'.
+sync-branch: "beads-sync"
+
+# Multi-repo configuration (experimental - bd-307)
+# Allows hydrating from multiple repositories and routing writes to the correct JSONL
+# repos:
+#   primary: "."  # Primary repo (where this database lives)
+#   additional:   # Additional repos to hydrate from (read-only)
+#     - ~/beads-planning  # Personal planning repo
+#     - ~/work-planning   # Work planning repo
+
+# Integration settings (access with 'bd config get/set')
+# These are stored in the database, not in this file:
+# - jira.url
+# - jira.project
+# - linear.url
+# - linear.api-key
+# - github.org
+# - github.repo

.beads/metadata.json

@@ -1,4 +1,4 @@
 {
   "database": "beads.db",
-  "jsonl_export": "issues.jsonl"
+  "jsonl_export": "sync_base.jsonl"
 }

.gitattributes

@@ -0,0 +1,3 @@
+
+# Use bd merge for beads JSONL files
+.beads/issues.jsonl merge=beads

flake.lock

@@ -21,6 +21,45 @@
         "type": "github"
       }
     },
+    "doomemacs": {
+      "flake": false,
+      "locked": {
+        "lastModified": 1767773143,
+        "narHash": "sha256-QL/t9v2kFNxBDyNJb/s411o3mxujan+QX5IZglTdpTk=",
+        "owner": "doomemacs",
+        "repo": "doomemacs",
+        "rev": "3e15fb36d7f94f0a218bda977be4d3f5da983a71",
+        "type": "github"
+      },
+      "original": {
+        "owner": "doomemacs",
+        "repo": "doomemacs",
+        "type": "github"
+      }
+    },
+    "emacs-overlay": {
+      "inputs": {
+        "nixpkgs": [
+          "nix-doom-emacs-unstraightened"
+        ],
+        "nixpkgs-stable": [
+          "nix-doom-emacs-unstraightened"
+        ]
+      },
+      "locked": {
+        "lastModified": 1768011937,
+        "narHash": "sha256-SnU2XTo34vwVaijs+4VwcXTNwMWO4nwzzs08N39UagA=",
+        "owner": "nix-community",
+        "repo": "emacs-overlay",
+        "rev": "79abf71d9897cf3b5189f7175cda1b1102abc65c",
+        "type": "github"
+      },
+      "original": {
+        "owner": "nix-community",
+        "repo": "emacs-overlay",
+        "type": "github"
+      }
+    },
     "flake-compat": {
       "flake": false,
       "locked": {
@@ -159,6 +198,27 @@
         "type": "github"
       }
     },
+    "nix-doom-emacs-unstraightened": {
+      "inputs": {
+        "doomemacs": "doomemacs",
+        "emacs-overlay": "emacs-overlay",
+        "nixpkgs": [],
+        "systems": "systems_2"
+      },
+      "locked": {
+        "lastModified": 1768034604,
+        "narHash": "sha256-62pIZMvGHhYJmMiiBsxHqZt/dFyENPcFHlJq5NJF3Sw=",
+        "owner": "marienz",
+        "repo": "nix-doom-emacs-unstraightened",
+        "rev": "9b3b8044fe4ccdcbb2d6f733d7dbe4d5feea18bc",
+        "type": "github"
+      },
+      "original": {
+        "owner": "marienz",
+        "repo": "nix-doom-emacs-unstraightened",
+        "type": "github"
+      }
+    },
     "nix-github-actions": {
       "inputs": {
         "nixpkgs": [
@@ -303,6 +363,7 @@
         "home-manager-unstable": "home-manager-unstable",
         "jovian": "jovian",
         "nix-darwin": "nix-darwin",
+        "nix-doom-emacs-unstraightened": "nix-doom-emacs-unstraightened",
         "nixos-wsl": "nixos-wsl",
         "nixpkgs": "nixpkgs_2",
         "nixpkgs-unstable": "nixpkgs-unstable",
@@ -324,6 +385,21 @@
         "repo": "default",
         "type": "github"
       }
+    },
+    "systems_2": {
+      "locked": {
+        "lastModified": 1681028828,
+        "narHash": "sha256-Vy1rq5AaRuLzOxct8nz4T6wlgyUR7zLU309k9mBC768=",
+        "owner": "nix-systems",
+        "repo": "default",
+        "rev": "da67096a3b9bf56a91d16901293e51ba5b49a27e",
+        "type": "github"
+      },
+      "original": {
+        "owner": "nix-systems",
+        "repo": "default",
+        "type": "github"
+      }
     }
   },
   "root": "root",

flake.nix

@@ -47,6 +47,12 @@
       url = "github:steveyegge/beads";
       inputs.nixpkgs.follows = "nixpkgs-unstable";
     };
+
+    nix-doom-emacs-unstraightened = {
+      url = "github:marienz/nix-doom-emacs-unstraightened";
+      # Don't follow nixpkgs to avoid rebuild issues with emacs-overlay
+      inputs.nixpkgs.follows = "";
+    };
   };
 
   outputs = { self, nixpkgs, nixpkgs-unstable, nixos-wsl, ... } @ inputs: let
@@ -70,6 +76,7 @@
         home-manager.useUserPackages = true;
         home-manager.sharedModules = [
           inputs.plasma-manager.homeModules.plasma-manager
+          inputs.nix-doom-emacs-unstraightened.homeModule
         ];
         home-manager.extraSpecialArgs = {
           globalInputs = inputs;
@@ -98,6 +105,7 @@
         home-manager.useUserPackages = true;
         home-manager.sharedModules = [
           inputs.plasma-manager-unstable.homeModules.plasma-manager
+          inputs.nix-doom-emacs-unstraightened.homeModule
         ];
         home-manager.extraSpecialArgs = {
           globalInputs = inputs;
@@ -129,6 +137,9 @@
         ];
         home-manager.useGlobalPkgs = true;
         home-manager.useUserPackages = true;
+        home-manager.sharedModules = [
+          inputs.nix-doom-emacs-unstraightened.homeModule
+        ];
         home-manager.extraSpecialArgs = {
           globalInputs = inputs;
         };

home/home-live-usb.nix

@@ -14,7 +14,12 @@
     desktop.enable = true;
     tmux.enable = true;
     plasma-manager.enable = true;
-    emacs.enable = true;
+    emacs = {
+      enable = true;
+      # Use pre-built Doom Emacs - all packages built at nix build time
+      # This means no doom sync is needed after booting the live USB
+      prebuiltDoom = true;
+    };
     i3_sway.enable = true;
     # development.enable = false;  # Not needed for live USB
     # communication.enable = false; # Not needed for live USB

home/roles/emacs/default.nix

@@ -23,55 +23,90 @@ let
     if pkgs.stdenv.isDarwin
     then pkgs.emacs-macport.pkgs.withPackages emacsPackages
     else pkgs.emacs.pkgs.withPackages emacsPackages;
+
+  # Path to doom config directory (relative to this file)
+  doomConfigDir = ./doom;
 in
 {
   options.home.roles.emacs = {
     enable = mkEnableOption "Doom Emacs with vterm and tree-sitter support";
+
+    prebuiltDoom = mkOption {
+      type = types.bool;
+      default = false;
+      description = ''
+        Use nix-doom-emacs-unstraightened to pre-build all Doom packages at
+        nix build time. This eliminates the need to run `doom sync` after
+        first boot, making it ideal for live USB images or immutable systems.
+
+        When enabled, the doom configuration is read-only (stored in nix store).
+      '';
+    };
   };
 
-  config = mkIf cfg.enable {
-    home.packages = [
-      pkgs.emacs-all-the-icons-fonts
-      pkgs.fira-code
-      pkgs.fontconfig
-      pkgs.graphviz
-      pkgs.isort
-      pkgs.nerd-fonts.fira-code
-      pkgs.nerd-fonts.droid-sans-mono
-      pkgs.nil # nix lsp language server
-      pkgs.nixfmt-rfc-style
-      (pkgs.ripgrep.override {withPCRE2 = true;})
-      pkgs.pipenv
-      pkgs.poetry
-      pkgs.python3
-    ];
+  config = mkIf cfg.enable (mkMerge [
+    # Common configuration for both modes
+    {
+      home.packages = [
+        pkgs.emacs-all-the-icons-fonts
+        pkgs.fira-code
+        pkgs.fontconfig
+        pkgs.graphviz
+        pkgs.isort
+        pkgs.nerd-fonts.fira-code
+        pkgs.nerd-fonts.droid-sans-mono
+        pkgs.nil # nix lsp language server
+        pkgs.nixfmt-rfc-style
+        (pkgs.ripgrep.override {withPCRE2 = true;})
+        pkgs.pipenv
+        pkgs.poetry
+        pkgs.python3
+      ];
 
-    programs.emacs = {
-      enable = true;
-      package = defaultEmacsPackage;
-    };
+      fonts.fontconfig.enable = true;
+    }
 
-    fonts.fontconfig.enable = true;
+    # Standard Doom Emacs mode (requires doom sync at runtime)
+    (mkIf (!cfg.prebuiltDoom) {
+      programs.emacs = {
+        enable = true;
+        package = defaultEmacsPackage;
+      };
 
-    # Mount emacs and tree-sitter grammars from nix store
-    home.file = {
-      "${config.xdg.configHome}/emacs".source = doomEmacs;
-    };
+      # Mount emacs and tree-sitter grammars from nix store
+      home.file = {
+        "${config.xdg.configHome}/emacs".source = doomEmacs;
+      };
 
-    home.sessionPath = [
-      "${config.xdg.configHome}/emacs/bin"
-    ];
+      home.sessionPath = [
+        "${config.xdg.configHome}/emacs/bin"
+      ];
 
-    home.sessionVariables = {
-      DOOMDIR = "${config.xdg.configHome}/doom";
-      DOOMLOCALDIR = "${config.xdg.dataHome}/doom";
-    };
+      home.sessionVariables = {
+        DOOMDIR = "${config.xdg.configHome}/doom";
+        DOOMLOCALDIR = "${config.xdg.dataHome}/doom";
+      };
 
-    # TODO: Use mkOutOfStoreSymlink instead?
-    home.activation.doomConfig = lib.hm.dag.entryAfter ["writeBoundary"] ''
-      # Always remove and recreate the symlink to ensure it points to the source directory
-      rm -rf "${config.xdg.configHome}/doom"
-      ln -sf "${config.home.homeDirectory}/nixos-configs/home/roles/emacs/doom" "${config.xdg.configHome}/doom"
-    '';
-  };
+      # TODO: Use mkOutOfStoreSymlink instead?
+      home.activation.doomConfig = lib.hm.dag.entryAfter ["writeBoundary"] ''
+        # Always remove and recreate the symlink to ensure it points to the source directory
+        rm -rf "${config.xdg.configHome}/doom"
+        ln -sf "${config.home.homeDirectory}/nixos-configs/home/roles/emacs/doom" "${config.xdg.configHome}/doom"
+      '';
+    })
+
+    # Pre-built Doom Emacs mode (no doom sync needed - ideal for live USB)
+    (mkIf cfg.prebuiltDoom {
+      programs.doom-emacs = {
+        enable = true;
+        doomDir = doomConfigDir;
+        doomLocalDir = "${config.xdg.dataHome}/doom";
+        # Add extra packages that aren't part of Doom but needed for our config
+        extraPackages = epkgs: [
+          epkgs.vterm
+          epkgs.treesit-grammars.with-all-grammars
+        ];
+      };
+    })
+  ]);
 }

home/roles/emacs/doom/packages.el

@@ -51,11 +51,21 @@
 
 ;; (package! org-caldav)
 
+;; Note: Packages with custom recipes must be pinned for nix-doom-emacs-unstraightened
+;; to build deterministically. Update pins when upgrading packages.
+
 (package! gptel :recipe (:nonrecursive t))
 
 (package! claude-code-ide
-  :recipe (:host github :repo "manzaltu/claude-code-ide.el"))
+  :recipe (:host github :repo "manzaltu/claude-code-ide.el")
+  :pin "760240d7f03ff16f90ede9d4f4243cd94f3fed73")
 
 (package! gptel-tool-library
   :recipe (:host github :repo "aard-fi/gptel-tool-library"
-           :files ("*.el")))
+           :files ("*.el"))
+  :pin "baffc3b0d74a2b7cbda0d5cd6dd7726d6ccaca83")
+
+(package! beads
+  :recipe (:type git :repo "https://codeberg.org/ctietze/beads.el.git"
+           :files ("lisp/*.el"))
+  :pin "f40a6461d3c0fa0969311bbb6a1e30d1bba86c88")

machines/john-endesktop/hardware-configuration.nix

@@ -18,12 +18,29 @@
   # File systems - these will need to be updated after installation
   # The nvme0n1p5 partition will be formatted as btrfs for NixOS root
   fileSystems."/" = {
-    # Update this device path after installation
-    device = "/dev/disk/by-uuid/CHANGE-THIS-TO-YOUR-UUID";
+    device = "/dev/disk/by-uuid/5f4ad025-bfab-4aed-a933-6638348059e5";
     fsType = "btrfs";
     options = [ "subvol=@" "compress=zstd" "noatime" ];
   };
 
+  fileSystems."/home" = {
+    device = "/dev/disk/by-uuid/5f4ad025-bfab-4aed-a933-6638348059e5";
+    fsType = "btrfs";
+    options = [ "subvol=@home" "compress=zstd" "noatime" ];
+  };
+
+  fileSystems."/nix" = {
+    device = "/dev/disk/by-uuid/5f4ad025-bfab-4aed-a933-6638348059e5";
+    fsType = "btrfs";
+    options = [ "subvol=@nix" "compress=zstd" "noatime" ];
+  };
+
+  fileSystems."/var/log" = {
+    device = "/dev/disk/by-uuid/5f4ad025-bfab-4aed-a933-6638348059e5";
+    fsType = "btrfs";
+    options = [ "subvol=@log" "compress=zstd" "noatime" ];
+  };
+
   fileSystems."/boot" = {
     # This should match your current EFI partition
     device = "/dev/disk/by-uuid/F5C6-D570";
@@ -35,10 +52,8 @@
   # The pools should be imported automatically via boot.zfs.extraPools
   # /media and /swarmvols will be mounted by ZFS
 
-  # Swap - using ZFS zvol
-  swapDevices = [
-    { device = "/dev/zvol/media/swap"; }
-  ];
+  # No swap needed - 23GB RAM is sufficient for this NFS/ZFS server
+  swapDevices = [ ];
 
   # CPU microcode
   hardware.cpu.intel.updateMicrocode = lib.mkDefault config.hardware.enableRedistributableFirmware;