feat: Move bootstrap/build-liveusb scripts to flake apps

- Move bootstrap.sh to scripts/ and add as flake app
- Move build-liveusb.sh to scripts/ and add as flake app
- Update usage comments to show nix run commands
- Improve build-liveusb.sh with better error handling (set -euo pipefail)
- Remove emojis from output messages for cleaner log output

Scripts can now be run consistently via:
  nix run .#bootstrap -- <hostname>
  nix run .#build-liveusb

Implements bead: nixos-configs-bli

.gitignore

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

build-liveusb.sh

@@ -1,19 +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
-
-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

@@ -21,6 +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;
         };
@@ -219,7 +230,11 @@
       system = "x86_64-linux";
       modules = nixosModules ++ [
         ./machines/john-endesktop/configuration.nix
-        # Minimal server - no home-manager needed
+        inputs.home-manager.nixosModules.home-manager
+        {
+          home-manager.users.johno = import ./home/home-server.nix;
+          home-manager.extraSpecialArgs = { inherit system; };
+        }
       ];
     };
 
@@ -260,6 +275,16 @@
           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"
+          ${builtins.readFile ./scripts/build-liveusb.sh}
+        '';
       in {
         update-doomemacs = {
           type = "app";
@@ -277,6 +302,14 @@
           type = "app";
           program = "${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

@@ -14,7 +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;
     starship.enable = true;
     # development.enable = false;  # Not needed for live USB

home/home-server.nix

@@ -10,6 +10,8 @@
   home.roles = {
     base.enable = true;
     development.enable = true;
+    emacs.enable = true;
+    starship.enable = true;
     tmux.enable = true;
   };
 

home/roles/development/default.nix

@@ -85,12 +85,17 @@ in
         fi
       done
 
-      # Copy local skills from this repo
+      # Copy local skills from this repo (with retry for race conditions with running Claude)
       for file in ${./skills}/*.md; do
         if [ -f "$file" ]; then
           filename=$(basename "$file" .md)
           dest="$HOME/.claude/commands/''${filename}.md"
-          cp "$file" "$dest"
+          # Remove existing file first, then copy with retry on failure
+          rm -f "$dest" 2>/dev/null || true
+          if ! cp "$file" "$dest" 2>/dev/null; then
+            sleep 0.5
+            cp "$file" "$dest" || echo "Warning: Failed to copy $filename.md to commands"
+          fi
         fi
       done
 

home/roles/development/skills/parallel_beads.md

@@ -93,7 +93,13 @@ Work on bead [BEAD_ID]: [BEAD_TITLE]
      - [List of changes made]"
      ```
 
-6. **Report results**:
+6. **Update bead status**:
+   - Mark the bead as "in_review": `bd update [BEAD_ID] --status=in_review`
+   - Add the PR URL to the bead notes: `bd update [BEAD_ID] --notes="$(bd show [BEAD_ID] --json | jq -r '.notes')
+
+PR: [PR_URL]"`
+
+7. **Report results**:
    - Return: PR URL, bead ID, success/failure status
    - If blocked or unable to complete, explain what's blocking progress
 ```
@@ -165,11 +171,11 @@ Example output:
 ```
 ## Parallel Beads Summary
 
-| Bead | PR | Status | Review |
+| Bead | PR | Bead Status | Review |
-|------|-----|--------|--------|
+|------|-----|-------------|--------|
-| beads-abc | #123 | Success | Approved |
+| beads-abc | #123 | in_review | Approved |
-| beads-xyz | #124 | Success | Needs changes |
+| beads-xyz | #124 | in_review | Needs changes |
-| beads-123 | - | Failed | Blocked by missing dependency |
+| beads-123 | - | open (failed) | Blocked by missing dependency |
 
 ### Failures/Blockers
 - beads-123: Could not complete because [reason]
@@ -177,6 +183,7 @@ Example output:
 ### Next Steps
 - Review PRs that need changes
 - Address blockers for failed beads
+- Run `/reconcile_beads` after PRs are merged to close beads
 ```
 
 ## Error Handling

home/roles/development/skills/reconcile_beads.md

@@ -0,0 +1,88 @@
+---
+description: Reconcile beads with merged PRs and close completed beads
+---
+
+# Reconcile Beads Workflow
+
+This skill reconciles beads that are in `in_review` status with their corresponding PRs. If a PR has been merged, the bead is closed.
+
+## Prerequisites
+
+- Custom status `in_review` must be configured: `bd config set status.custom "in_review"`
+- Beads in `in_review` status should have a PR URL in their notes
+
+## Workflow
+
+### Step 1: Find beads in review
+
+```bash
+bd list --status=in_review
+```
+
+### Step 2: For each bead, check PR status
+
+1. **Get the PR URL from bead notes**:
+   ```bash
+   bd show [BEAD_ID] --json | jq -r '.[0].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 number: `echo "$NOTES" | grep -oP '/pulls/\K\d+'`
+
+2. **Detect hosting provider**:
+   - Run `git remote get-url origin`
+   - If URL contains `github.com`, use `gh`; otherwise use `tea` (Gitea/Forgejo)
+
+3. **Check PR status**:
+   - For GitHub:
+     ```bash
+     gh pr view [PR_NUMBER] --json state,merged
+     ```
+   - For Gitea:
+     ```bash
+     tea pr list --state=closed
+     ```
+     Look for the PR number in the INDEX column with STATE "merged".
+     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
+
+If the PR is merged:
+```bash
+bd close [BEAD_ID] --reason="PR merged: [PR_URL]"
+```
+
+### Step 4: Report summary
+
+Present results:
+
+```
+## Beads Reconciliation Summary
+
+### Closed (PR Merged)
+| Bead | PR | Title |
+|------|-----|-------|
+| beads-abc | #123 | Feature X |
+| beads-xyz | #456 | Bug fix Y |
+
+### Still in Review
+| Bead | PR | Status | Title |
+|------|-----|--------|-------|
+| beads-def | #789 | Open | Feature Z |
+
+### Issues Found
+- beads-ghi: No PR URL found in notes
+- beads-jkl: PR #999 not found (may have been deleted)
+```
+
+## Error Handling
+
+- **Missing PR URL**: Skip the bead and report it
+- **PR not found**: Report the error but continue with other beads
+- **API errors**: Report and continue
+
+## Notes
+
+- This skill complements `/parallel_beads` which sets beads to `in_review` status
+- Run this skill periodically or after merging PRs to keep beads in sync
+- Beads with closed (but not merged) PRs are not automatically closed - they may need rework

home/roles/emacs/default.nix

@@ -23,13 +23,30 @@ 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 {
+  config = mkIf cfg.enable (mkMerge [
+    # Common configuration for both modes
+    {
       home.packages = [
         pkgs.emacs-all-the-icons-fonts
         pkgs.fira-code
@@ -46,13 +63,16 @@ 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 = {
         "${config.xdg.configHome}/emacs".source = doomEmacs;
@@ -73,5 +93,20 @@ in
         rm -rf "${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

@@ -51,11 +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")

scripts/bootstrap.sh

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

scripts/build-liveusb.sh

@@ -0,0 +1,22 @@
+#!/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