feat(skills): Improve parallel beads workflow with in_review status

- Add step to mark beads as 'in_review' after PR creation
- Add PR URL to bead notes for traceability
- Create reconcile_beads skill to close beads when PRs are merged
- Update summary table to show bead status instead of generic status

Implements bead: nixos-configs-85h

.gitignore

@@ -1,3 +1,2 @@
 result
 thoughts
-.beads

bootstrap.sh

@@ -1,7 +1,6 @@
 #!/usr/bin/env bash
 # bootstrap.sh
-# Usage: nix run .#bootstrap -- <hostname>
+# Usage: sudo ./bootstrap.sh <hostname>
-# Or: sudo ./scripts/bootstrap.sh <hostname>
 set -euo pipefail
 
 NEW_HOSTNAME="${1:?missing hostname}"
@@ -9,3 +8,4 @@ FLAKE_URI="git+https://git.johnogle.info/johno/nixos-configs.git#${NEW_HOSTNAME}
 
 export NIX_CONFIG="experimental-features = nix-command flakes"
 nixos-rebuild switch --flake "$FLAKE_URI"
+

build-liveusb.sh

@@ -0,0 +1,19 @@
+#!/usr/bin/env bash
+
+# Build Live USB ISO from flake configuration
+# Creates an uncompressed ISO suitable for Ventoy and other USB boot tools
+
+set -e
+
+echo "Building Live USB ISO..."
+nix build .#nixosConfigurations.live-usb.config.system.build.isoImage --show-trace
+
+if [ -f "./result/iso/"*.iso ]; then
+    iso_file=$(ls ./result/iso/*.iso)
+    echo "✅ Build complete!"
+    echo "📁 ISO location: $iso_file"
+    echo "💾 Ready for Ventoy or dd to USB"
+else
+    echo "❌ Build failed - no ISO file found"
+    exit 1
+fi

flake.lock

@@ -21,45 +21,6 @@
         "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": {
@@ -198,27 +159,6 @@
         "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": [
@@ -363,7 +303,6 @@
         "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",
@@ -385,21 +324,6 @@
         "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

@@ -47,12 +47,6 @@
       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
@@ -76,7 +70,6 @@
         home-manager.useUserPackages = true;
         home-manager.sharedModules = [
           inputs.plasma-manager.homeModules.plasma-manager
-          inputs.nix-doom-emacs-unstraightened.homeModule
         ];
         home-manager.extraSpecialArgs = {
           globalInputs = inputs;
@@ -105,7 +98,6 @@
         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;
@@ -137,9 +129,6 @@
         ];
         home-manager.useGlobalPkgs = true;
         home-manager.useUserPackages = true;
-        home-manager.sharedModules = [
-          inputs.nix-doom-emacs-unstraightened.homeModule
-        ];
         home-manager.extraSpecialArgs = {
           globalInputs = inputs;
         };
@@ -275,16 +264,6 @@
           export PATH="${pkgs.lib.makeBinPath commonDeps}:$PATH"
           ${builtins.readFile ./scripts/upgrade.sh}
         '';
-
-        bootstrap = pkgs.writeShellScriptBin "bootstrap" ''
-          export PATH="${pkgs.lib.makeBinPath commonDeps}:$PATH"
-          ${builtins.readFile ./scripts/bootstrap.sh}
-        '';
-
-        build-liveusb = pkgs.writeShellScriptBin "build-liveusb" ''
-          export PATH="${pkgs.lib.makeBinPath commonDeps}:$PATH"
-          ${builtins.readFile ./scripts/build-liveusb.sh}
-        '';
       in {
         update-doomemacs = {
           type = "app";
@@ -302,14 +281,6 @@
           type = "app";
           program = "${upgrade}/bin/upgrade";
         };
-        bootstrap = {
-          type = "app";
-          program = "${bootstrap}/bin/bootstrap";
-        };
-        build-liveusb = {
-          type = "app";
-          program = "${build-liveusb}/bin/build-liveusb";
-        };
       }
     );
   };

home/home-live-usb.nix

@@ -14,12 +14,7 @@
     desktop.enable = true;
     tmux.enable = true;
     plasma-manager.enable = true;
-    emacs = {
+    emacs.enable = true;
-      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;
     starship.enable = true;
     # development.enable = false;  # Not needed for live USB

home/roles/development/skills/reconcile_beads.md

@@ -23,11 +23,9 @@ bd list --status=in_review
 
 1. **Get the PR URL from bead notes**:
    ```bash
-   bd show [BEAD_ID] --json | jq -r '.[0].notes'
+   bd show [BEAD_ID] --json | jq -r '.notes'
    ```
-   Note: `bd show --json` returns an array, so use `.[0]` to access the first element.
+   Extract the PR URL (look for lines starting with "PR:" or containing pull request URLs)
-   Extract the PR URL (look for lines starting with "PR:" or containing pull request URLs).
-   Extract the PR number: `echo "$NOTES" | grep -oP '/pulls/\K\d+'`
 
 2. **Detect hosting provider**:
    - Run `git remote get-url origin`
@@ -40,10 +38,9 @@ bd list --status=in_review
      ```
    - For Gitea:
      ```bash
-     tea pr list --state=closed
+     tea pr view [PR_NUMBER]
      ```
-     Look for the PR number in the INDEX column with STATE "merged".
+     Look for "State: merged" or "State: closed"
-     Note: `tea pr view [PR_NUMBER]` lists all PRs, not a specific one. Use `tea pr list --state=closed` and look for your PR number in the results.
 
 ### Step 3: Close merged beads
 

home/roles/emacs/default.nix

@@ -23,30 +23,13 @@ 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 (mkMerge [
+  config = mkIf cfg.enable {
-    # Common configuration for both modes
-    {
     home.packages = [
       pkgs.emacs-all-the-icons-fonts
       pkgs.fira-code
@@ -63,16 +46,13 @@ in
       pkgs.python3
     ];
 
-      fonts.fontconfig.enable = true;
-    }
-
-    # Standard Doom Emacs mode (requires doom sync at runtime)
-    (mkIf (!cfg.prebuiltDoom) {
     programs.emacs = {
       enable = true;
       package = defaultEmacsPackage;
     };
 
+    fonts.fontconfig.enable = true;
+
     # Mount emacs and tree-sitter grammars from nix store
     home.file = {
       "${config.xdg.configHome}/emacs".source = doomEmacs;
@@ -93,20 +73,5 @@ in
       rm -rf "${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

@@ -51,21 +51,11 @@
 
 ;; (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")

scripts/build-liveusb.sh

@@ -1,22 +0,0 @@
-#!/usr/bin/env bash
-# Build Live USB ISO from flake configuration
-# Creates an uncompressed ISO suitable for Ventoy and other USB boot tools
-# Usage: nix run .#build-liveusb
-# Or: ./scripts/build-liveusb.sh
-
-set -euo pipefail
-
-REPO_ROOT="${REPO_ROOT:-$(git rev-parse --show-toplevel 2>/dev/null || pwd)}"
-
-echo "Building Live USB ISO..."
-nix build "${REPO_ROOT}#nixosConfigurations.live-usb.config.system.build.isoImage" --show-trace
-
-if ls "${REPO_ROOT}/result/iso/"*.iso 1> /dev/null 2>&1; then
-    iso_file=$(ls "${REPO_ROOT}/result/iso/"*.iso)
-    echo "Build complete!"
-    echo "ISO location: $iso_file"
-    echo "Ready for Ventoy or dd to USB"
-else
-    echo "Build failed - no ISO file found"
-    exit 1
-fi