Extract shared NixOS/Darwin base config into roles/common.nix

Create roles/common.nix containing shared configuration between NixOS and
Darwin: timezone, base packages (git, glances, pciutils, tree, usbutils, vim),
nix settings (experimental-features, max-jobs, trusted-users), gc config,
and allowUnfree setting.

Both roles/default.nix and roles/darwin.nix now import common.nix and only
contain platform-specific configuration.

.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

@@ -0,0 +1,4 @@
+{
+  "database": "beads.db",
+  "jsonl_export": "sync_base.jsonl"
+}

.gitattributes

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

AGENTS.md

@@ -200,4 +200,30 @@ tea issues close --repo johno/nixos-configs 2
 
 ## Important Notes
 
-- **Sudo access**: Claude Code does not have sudo access. Ask the user to run elevated commands like `sudo nixos-rebuild switch`
+- **Sudo access**: Claude Code does not have sudo access. Ask the user to run elevated commands like `sudo nixos-rebuild switch`
+
+## Landing the Plane (Session Completion)
+
+**When ending a work session**, you MUST complete ALL steps below. Work is NOT complete until `git push` succeeds.
+
+**MANDATORY WORKFLOW:**
+
+1. **File issues for remaining work** - Create issues for anything that needs follow-up
+2. **Run quality gates** (if code changed) - Tests, linters, builds
+3. **Update issue status** - Close finished work, update in-progress items
+4. **PUSH TO REMOTE** - This is MANDATORY:
+   ```bash
+   git pull --rebase
+   bd sync
+   git push
+   git status  # MUST show "up to date with origin"
+   ```
+5. **Clean up** - Clear stashes, prune remote branches
+6. **Verify** - All changes committed AND pushed
+7. **Hand off** - Provide context for next session
+
+**CRITICAL RULES:**
+- Work is NOT complete until `git push` succeeds
+- NEVER stop before pushing - that leaves work stranded locally
+- NEVER say "ready to push when you are" - YOU must push
+- If push fails, resolve and retry until it succeeds

flake.lock

@@ -1,5 +1,26 @@
 {
   "nodes": {
+    "beads": {
+      "inputs": {
+        "flake-utils": "flake-utils",
+        "nixpkgs": [
+          "nixpkgs-unstable"
+        ]
+      },
+      "locked": {
+        "lastModified": 1767911810,
+        "narHash": "sha256-0L4ATr01UsmBC0rSW62VIMVVSUihAQu2+ZOoHk9BQnA=",
+        "owner": "steveyegge",
+        "repo": "beads",
+        "rev": "28ff9fe9919a9665a0f00f5b3fcd084b43fb6cc3",
+        "type": "github"
+      },
+      "original": {
+        "owner": "steveyegge",
+        "repo": "beads",
+        "type": "github"
+      }
+    },
     "flake-compat": {
       "flake": false,
       "locked": {
@@ -16,6 +37,24 @@
         "type": "github"
       }
     },
+    "flake-utils": {
+      "inputs": {
+        "systems": "systems"
+      },
+      "locked": {
+        "lastModified": 1731533236,
+        "narHash": "sha256-l0KFg5HjrsfsO/JpG+r7fRrqm12kzFHyUHqHCVpMMbI=",
+        "owner": "numtide",
+        "repo": "flake-utils",
+        "rev": "11707dc2f618dd54ca8739b309ec4fc024de578b",
+        "type": "github"
+      },
+      "original": {
+        "owner": "numtide",
+        "repo": "flake-utils",
+        "type": "github"
+      }
+    },
     "google-cookie-retrieval": {
       "inputs": {
         "nixpkgs": [
@@ -258,6 +297,7 @@
     },
     "root": {
       "inputs": {
+        "beads": "beads",
         "google-cookie-retrieval": "google-cookie-retrieval",
         "home-manager": "home-manager",
         "home-manager-unstable": "home-manager-unstable",
@@ -269,6 +309,21 @@
         "plasma-manager": "plasma-manager",
         "plasma-manager-unstable": "plasma-manager-unstable"
       }
+    },
+    "systems": {
+      "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

@@ -42,6 +42,11 @@
       url = "github:Jovian-Experiments/Jovian-NixOS";
       inputs.nixpkgs.follows = "nixpkgs-unstable";
     };
+
+    beads = {
+      url = "github:steveyegge/beads";
+      inputs.nixpkgs.follows = "nixpkgs-unstable";
+    };
   };
 
   outputs = { self, nixpkgs, nixpkgs-unstable, nixos-wsl, ... } @ inputs: let

home/roles/development/default.nix

@@ -5,7 +5,7 @@ with lib;
 let
   cfg = config.home.roles.development;
 
-  # Fetch the claude-plugins repository
+  # Fetch the claude-plugins repository (for humanlayer commands/agents)
   # Update the rev to get newer versions of the commands
   claudePluginsRepo = builtins.fetchGit {
     url = "https://github.com/jeffh/claude-plugins.git";
@@ -14,6 +14,7 @@ let
     rev = "5e3e4d937162185b6d78c62022cbfd1c8ad42c4c";
     ref = "main";
   };
+
 in
 {
   options.home.roles.development = {
@@ -36,12 +37,14 @@ in
 
   config = mkIf cfg.enable {
     home.packages = [
+      globalInputs.beads.packages.${system}.default
       pkgs.unstable.claude-code
       pkgs.unstable.claude-code-router
       pkgs.unstable.codex
 
       # Custom packages
       pkgs.custom.tea-rbw
+      pkgs.custom.perles
     ];
 
     # Install Claude Code humanlayer command and agent plugins
@@ -89,6 +92,16 @@ in
       }"
     '';
 
+    # Set up beads Claude Code integration (hooks for SessionStart/PreCompact)
+    # This uses the CLI + hooks approach which is recommended over MCP for Claude Code
+    home.activation.claudeCodeBeadsSetup = lib.hm.dag.entryAfter ["writeBoundary" "claudeCodeCommands"] ''
+      # Run bd setup claude to install hooks into ~/.claude/settings.json
+      # This is idempotent - safe to run multiple times
+      ${globalInputs.beads.packages.${system}.default}/bin/bd setup claude 2>/dev/null || true
+
+      $DRY_RUN_CMD echo "Claude Code beads integration configured (hooks installed)"
+    '';
+
     # Note: modules must be imported at top-level home config
   };
 }

home/roles/emacs/doom/config.el

@@ -71,7 +71,10 @@
         org-journal-file-format "%Y-%m-%d.org"
         org-capture-templates
           '(("t" "Todo" entry (file+headline "~/org/todo.org" "Inbox")
-             "* TODO %? \n %i \n%a" :prepend t))))
+             "* TODO %? \n %i \n%a" :prepend t)))
+  ;; Make blocked tasks more visible in agenda (they have subtasks to do!)
+  (custom-set-faces!
+    '(org-agenda-dimmed-todo-face :foreground "#bb9af7" :weight normal)))
 
 (map! :after org-agenda
       :map org-agenda-mode-map
@@ -145,12 +148,24 @@
    :args (list '(:name "dirpath" :type "string" :description "Directory path to list"))))
 
 (use-package! claude-code-ide
-  :defer t
-  :config
-  (claude-code-ide-emacs-tools-setup)
+  :commands (claude-code-ide-menu claude-code-ide-open-here)
+  :init
   (map! :leader
         (:prefix ("o" . "open")
-         :desc "Claude Code IDE" "c" #'claude-code-ide-menu)))
+         :desc "Claude Code IDE" "c" #'claude-code-ide-menu))
+  :config
+  (claude-code-ide-emacs-tools-setup)
+  (setq claude-code-ide-cli-path "claude"
+        claude-code-ide-cli-extra-flags "--dangerously-skip-permissions"
+        claude-code-ide-focus-claude-after-ediff t
+        claude-code-ide-focus-on-open t
+        claude-code-ide-show-claude-window-in-ediff t
+        claude-code-ide-switch-tab-on-ediff t
+        claude-code-ide-use-ide-diff t
+        claude-code-ide-use-side-window t
+        claude-code-ide-window-height 20
+        claude-code-ide-window-side 'right
+        claude-code-ide-window-width 90))
 
 (after! gptel
   (require 'gptel-tool-library)

home/roles/i3+sway/default.nix

@@ -14,6 +14,7 @@ let
 
     keybindings = {
       "${shared_config.modifier}+Return" = "exec ${terminal}";
+      "${shared_config.modifier}+Shift+Return" = "exec ${cfg.browser}";
       "${shared_config.modifier}+Shift+q" = "kill";
 
       "${shared_config.modifier}+a" = "focus parent";
@@ -98,6 +99,12 @@ in {
   options.home.roles.i3_sway = {
     enable = mkEnableOption "i3 and Sway tiling window managers with waybar and rofi";
 
+    browser = mkOption {
+      type = types.str;
+      default = "firefox --new-window";
+      description = "Browser to use for new window keybinding";
+    };
+
     extraSharedConfig = mkOption {
       type = types.attrs;
       default = {};

machines/john-endesktop/MIGRATION_PLAN.md

@@ -170,6 +170,7 @@ This document outlines the plan to migrate the john-endesktop server from Arch L
    ```bash
    blkid /dev/nvme0n1p5
    # Note the UUID for updating hardware-configuration.nix
+/dev/nvme0n1p5: LABEL="nixos" UUID="5f4ad025-bfab-4aed-a933-6638348059e5" UUID_SUB="4734d820-7b8a-4b7f-853a-026021c1d204" BLOCK_SIZE="4096" TYPE="btrfs" PARTLABEL="data" PARTUUID="9ea025df-cdb7-48fd-b5d4-37cd5d8588eb"
    ```
 
 8. **Copy your NixOS configuration to the server**
@@ -388,11 +389,11 @@ After successful migration and 24-48 hours of stable operation:
 
 Pre-migration:
 - [x] nvme0n1p5 removal from media pool complete
-- [ ] Recent backup verified (< 24 hours)
-- [ ] Maintenance window scheduled
-- [ ] NixOS ISO downloaded
-- [ ] Bootable USB created
-- [ ] NixOS config builds successfully
+- [x] Recent backup verified (< 24 hours)
+- [x] Maintenance window scheduled
+- [x] NixOS ISO downloaded
+- [x] Bootable USB created
+- [x] NixOS config builds successfully
 
 During migration:
 - [ ] ZFS pools exported

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;

packages/default.nix

@@ -4,4 +4,5 @@
   tea-rbw = pkgs.callPackage ./tea-rbw {};
   app-launcher-server = pkgs.callPackage ./app-launcher-server {};
   claude-code = pkgs.callPackage ./claude-code {};
+  perles = pkgs.callPackage ./perles {};
 }

packages/perles/default.nix

@@ -0,0 +1,26 @@
+{ lib, buildGoModule, fetchFromGitHub }:
+
+buildGoModule rec {
+  pname = "perles";
+  version = "unstable-2025-01-09";
+
+  src = fetchFromGitHub {
+    owner = "zjrosen";
+    repo = "perles";
+    rev = "main";
+    hash = "sha256-JgRayb4+mJ1r0AtdnQfqAw2+QRte+licsfZOaRgYqcs=";
+  };
+
+  vendorHash = "sha256-R7UWTdBuPteneRqxrWK51nqLtZwDsqQoMAcohN4fyak=";
+
+  # Tests require a real git repository context
+  doCheck = false;
+
+  meta = with lib; {
+    description = "A TUI for the Beads issue tracking system with BQL query language";
+    homepage = "https://github.com/zjrosen/perles";
+    license = licenses.mit;
+    maintainers = [ ];
+    mainProgram = "perles";
+  };
+}

roles/common.nix

@@ -0,0 +1,35 @@
+# Common configuration shared between NixOS and Darwin
+{ lib, pkgs, ... }:
+
+{
+  config = {
+    time.timeZone = "America/Los_Angeles";
+
+    environment.systemPackages = with pkgs; [
+      git
+      glances
+      pciutils
+      tree
+      usbutils
+      vim
+    ];
+
+    nix = {
+      package = pkgs.nix;
+      settings = {
+        experimental-features = [ "nix-command" "flakes" ];
+        max-jobs = "auto";
+        trusted-users = [ "johno" ];
+        substituters = [
+        ];
+      };
+
+      gc = {
+        automatic = true;
+        options = "--delete-older-than 10d";
+      };
+    };
+
+    nixpkgs.config.allowUnfree = true;
+  };
+}

roles/darwin.nix

@@ -7,6 +7,10 @@ let
   setEnvironmentPath = "${config.system.build.setEnvironment}";
 in
 {
+  imports = [
+    ./common.nix
+  ];
+
   config = {
     # Salt manages /etc/bashrc, /etc/zshrc, /etc/zshenv
     # nix-darwin writes to .local variants for nix-specific configuration
@@ -43,8 +47,6 @@ in
       fi
     '';
 
-    time.timeZone = "America/Los_Angeles";
-
     # System preferences
     system.defaults = {
       # Custom keyboard shortcuts
@@ -79,42 +81,5 @@ in
         };
       };
     };
-
-    environment.systemPackages = with pkgs; [
-      git
-      glances
-      pciutils
-      tree
-      usbutils
-      vim
-    ];
-
-    nix = {
-      package = pkgs.nix;
-      # distributedBuilds = true;
-      # buildMachines = [{
-      #   hostName = "z790prors.oglehome";
-      #   system = "x86_64-linux";
-      #   protocol = "ssh-ng";
-      #   sshUser = "johno";
-      #   sshKey = "/root/.ssh/id_ed25519";
-      #   maxJobs = 3;
-      #   speedFactor = 2;
-      # }];
-      settings = {
-        experimental-features = [ "nix-command" "flakes" ];
-        max-jobs = "auto";
-        trusted-users = [ "johno" ];
-        substituters = [
-        ];
-      };
-
-      gc = {
-        automatic = true;
-        options = "--delete-older-than 10d";
-      };
-    };
-
-    nixpkgs.config.allowUnfree = true;
   };
-}
+}

roles/default.nix

@@ -4,6 +4,7 @@ with lib;
 
 {
   imports = [
+    ./common.nix
     ./audio
     ./bluetooth
     ./btrfs
@@ -31,7 +32,6 @@ with lib;
       LC_TELEPHONE = "en_US.UTF-8";
       LC_TIME = "en_US.UTF-8";
     };
-    time.timeZone = "America/Los_Angeles";
 
     services.xserver.xkb = {
       layout = "us";
@@ -49,42 +49,7 @@ with lib;
     # Enable the OpenSSH daemon.
     services.openssh.enable = true;
 
-    environment.systemPackages = with pkgs; [
-      git
-      glances
-      pciutils
-      tree
-      usbutils
-      vim
-    ];
-
-    nix = {
-      package = pkgs.nix;
-      # distributedBuilds = true;
-      # buildMachines = [{
-      #   hostName = "z790prors.oglehome";
-      #   system = "x86_64-linux";
-      #   protocol = "ssh-ng";
-      #   sshUser = "johno";
-      #   sshKey = "/root/.ssh/id_ed25519";
-      #   maxJobs = 3;
-      #   speedFactor = 2;
-      # }];
-      settings = {
-        experimental-features = [ "nix-command" "flakes" ];
-        max-jobs = "auto";
-        trusted-users = [ "johno" ];
-        substituters = [
-        ];
-      };
-
-      gc = {
-        automatic = true;
-        randomizedDelaySec = "14m";
-        options = "--delete-older-than 10d";
-      };
-    };
-
-    nixpkgs.config.allowUnfree = true;
+    # NixOS-specific gc option (not available on Darwin)
+    nix.gc.randomizedDelaySec = "14m";
   };
 }