feat(skills): Add batch research+plan skill for multiple beads

feat(skills): Close Gitea issues when beads are reconciled
Remove wixos (WSL) configuration
2026-01-14 14:00:30 -08:00 · 2026-01-14 13:59:30 -08:00 · 2026-01-13 18:02:36 -08:00 · 2026-01-13 17:48:36 -08:00 · 2026-01-13 17:48:00 -08:00 · 2026-01-13 17:20:59 -08:00
17 changed files with 591 additions and 253 deletions
--- a/.goosehints
+++ b/.goosehints
@@ -9,7 +9,7 @@ Directory Structure:
 ----------------------
 • packages/      - Custom Nix packages leveraged across various configurations.
 • roles/         - Role-based configurations (e.g., kodi, bluetooth) each with its own module (default.nix) for inclusion in machine setups.
-• machines/      - Machine-specific configurations (e.g., nix-book, z790prors, boxy, wixos) including configuration.nix and hardware-configuration.nix tailored for each hardware.
+• machines/      - Machine-specific configurations (e.g., nix-book, zix790prors, boxy) including configuration.nix and hardware-configuration.nix tailored for each hardware.
 • home/          - Home-manager configurations for personal environments and application settings (e.g., home-nix-book.nix, home-z790prors.nix).

 Design Principles:
--- a/AGENTS.md
+++ b/AGENTS.md
@@ -14,7 +14,7 @@ This repository uses `beads` for issue tracking and management. Run `bd quicksta

 ### Flake Structure
 - **flake.nix**: Main entry point defining inputs (nixpkgs, home-manager, plasma-manager, etc.) and outputs for multiple NixOS configurations
- **Machines**: `nix-book`, `boxy`, `wixos` (WSL configuration), `zix790prors`, `live-usb`, `johno-macbookpro` (Darwin/macOS)
+- **Machines**: `nix-book`, `boxy`, `zix790prors`, `live-usb`, `johno-macbookpro` (Darwin/macOS)
 - **Home configurations**: Standalone home-manager configuration for user `johno`

 ### Directory Structure
@@ -78,7 +78,6 @@ The repository also uses a modular home-manager role system for user-space confi
 - **nix-book**: Compact laptop → excludes office/media roles due to SSD space constraints
 - **boxy**: Living room media center → optimized for media consumption, excludes sync/office (shared machine)
 - **zix790prors**: All-purpose workstation → full desktop experience with all roles enabled
- **wixos**: WSL2 development → full desktop experience, inherits from zix790prors Windows host
 - **live-usb**: Temporary environment → only base + desktop roles, no persistent services
 - **johno-macbookpro**: macOS work laptop → Darwin-specific configuration with development tools

@@ -111,7 +110,6 @@ darwin-rebuild build --flake .#johno-macbookpro
 - `nix-book`: Compact laptop with storage constraints, uses `home/home-laptop-compact.nix`
 - `boxy`: Shared living room media center/gaming desktop with AMD GPU, uses `home/home-media-center.nix`
 - `zix790prors`: Powerful all-purpose workstation (gaming, 3D modeling, development), dual-boots Windows 11 with shared btrfs /games partition, uses `home/home-desktop.nix`
- `wixos`: WSL2 development environment running in Windows partition of zix790prors, uses `home/home-desktop.nix`
 - `live-usb`: Bootable ISO configuration, uses `home/home-live-usb.nix`
 - `johno-macbookpro`: macOS work laptop, uses `home/home-darwin-work.nix`

--- a/flake.lock
+++ b/flake.lock
@@ -60,22 +60,6 @@
        "type": "github"
      }
    },
-    "flake-compat": {
-      "flake": false,
-      "locked": {
-        "lastModified": 1765121682,
-        "narHash": "sha256-4VBOP18BFeiPkyhy9o4ssBNQEvfvv1kXkasAYd0+rrA=",
-        "owner": "edolstra",
-        "repo": "flake-compat",
-        "rev": "65f23138d8d09a92e30f1e5c87611b23ef451bf3",
-        "type": "github"
-      },
-      "original": {
-        "owner": "edolstra",
-        "repo": "flake-compat",
-        "type": "github"
-      }
-    },
    "flake-utils": {
      "inputs": {
        "systems": "systems"
@@ -241,38 +225,18 @@
        "type": "github"
      }
    },
-    "nixos-wsl": {
-      "inputs": {
-        "flake-compat": "flake-compat",
-        "nixpkgs": "nixpkgs"
-      },
-      "locked": {
-        "lastModified": 1765841014,
-        "narHash": "sha256-55V0AJ36V5Egh4kMhWtDh117eE3GOjwq5LhwxDn9eHg=",
-        "owner": "nix-community",
-        "repo": "NixOS-WSL",
-        "rev": "be4af8042e7a61fa12fda58fe9a3b3babdefe17b",
-        "type": "github"
-      },
-      "original": {
-        "owner": "nix-community",
-        "ref": "main",
-        "repo": "NixOS-WSL",
-        "type": "github"
-      }
-    },
    "nixpkgs": {
      "locked": {
-        "lastModified": 1765472234,
-        "narHash": "sha256-9VvC20PJPsleGMewwcWYKGzDIyjckEz8uWmT0vCDYK0=",
-        "owner": "NixOS",
+        "lastModified": 1767480499,
+        "narHash": "sha256-8IQQUorUGiSmFaPnLSo2+T+rjHtiNWc+OAzeHck7N48=",
+        "owner": "nixos",
        "repo": "nixpkgs",
-        "rev": "2fbfb1d73d239d2402a8fe03963e37aab15abe8b",
+        "rev": "30a3c519afcf3f99e2c6df3b359aec5692054d92",
        "type": "github"
      },
      "original": {
-        "owner": "NixOS",
-        "ref": "nixos-unstable",
+        "owner": "nixos",
+        "ref": "nixos-25.11",
        "repo": "nixpkgs",
        "type": "github"
      }
@@ -293,22 +257,6 @@
        "type": "github"
      }
    },
-    "nixpkgs_2": {
-      "locked": {
-        "lastModified": 1767480499,
-        "narHash": "sha256-8IQQUorUGiSmFaPnLSo2+T+rjHtiNWc+OAzeHck7N48=",
-        "owner": "nixos",
-        "repo": "nixpkgs",
-        "rev": "30a3c519afcf3f99e2c6df3b359aec5692054d92",
-        "type": "github"
-      },
-      "original": {
-        "owner": "nixos",
-        "ref": "nixos-25.11",
-        "repo": "nixpkgs",
-        "type": "github"
-      }
-    },
    "plasma-manager": {
      "inputs": {
        "home-manager": [
@@ -364,8 +312,7 @@
        "jovian": "jovian",
        "nix-darwin": "nix-darwin",
        "nix-doom-emacs-unstraightened": "nix-doom-emacs-unstraightened",
-        "nixos-wsl": "nixos-wsl",
-        "nixpkgs": "nixpkgs_2",
+        "nixpkgs": "nixpkgs",
        "nixpkgs-unstable": "nixpkgs-unstable",
        "plasma-manager": "plasma-manager",
        "plasma-manager-unstable": "plasma-manager-unstable"
--- a/flake.nix
+++ b/flake.nix
@@ -4,8 +4,7 @@
  inputs = {
    nixpkgs.url = "github:nixos/nixpkgs/nixos-25.11";
    nixpkgs-unstable.url = "github:nixos/nixpkgs/nixos-unstable";
-    nixos-wsl.url = "github:nix-community/NixOS-WSL/main";
-    
+
    nix-darwin = {
      url = "github:nix-darwin/nix-darwin/nix-darwin-25.11";
      inputs.nixpkgs.follows = "nixpkgs";
@@ -55,7 +54,7 @@
    };
  };

-  outputs = { self, nixpkgs, nixpkgs-unstable, nixos-wsl, ... } @ inputs: let
+  outputs = { self, nixpkgs, nixpkgs-unstable, ... } @ inputs: let
    # Shared overlay function to reduce duplication across module sets
    # Parameters:
    #   unstableOverlays: Additional overlays to apply when importing nixpkgs-unstable
@@ -84,6 +83,7 @@
      };
    };

+
    nixosModules = [
      ./roles
      inputs.home-manager.nixosModules.home-manager
@@ -157,24 +157,10 @@
      ];
    };

-    nixosConfigurations.wixos = nixpkgs.lib.nixosSystem rec {
-      system = "x86_64-linux";
-      modules = nixosModules ++ [
-        nixos-wsl.nixosModules.default
-        ./machines/wixos/configuration.nix
-        inputs.home-manager.nixosModules.home-manager
-        {
-          home-manager.users.johno = import ./home/home-desktop.nix;
-          home-manager.extraSpecialArgs = { inherit system; };
-        }
-      ];
-    };
-
    nixosConfigurations.zix790prors = nixpkgs.lib.nixosSystem rec {
      system = "x86_64-linux";
      modules = nixosModules ++ [
        ./machines/zix790prors/configuration.nix
-        inputs.home-manager.nixosModules.home-manager
        {
          home-manager.users.johno = import ./home/home-desktop.nix;
          home-manager.extraSpecialArgs = { inherit system; };
--- a/home/roles/communication/default.nix
+++ b/home/roles/communication/default.nix
@@ -4,6 +4,7 @@ with lib;

 let
  cfg = config.home.roles.communication;
+  isLinux = pkgs.stdenv.isLinux;
 in
 {
  options.home.roles.communication = {
@@ -12,14 +13,14 @@ in

  config = mkIf cfg.enable {
    home.packages = [
-      # Communication apps
+      # For logging back into google chat (cross-platform)
+      globalInputs.google-cookie-retrieval.packages.${system}.default
+    ] ++ optionals isLinux [
+      # Linux-only communication apps (Electron apps don't build on Darwin)
      pkgs.element-desktop
      # Re-enabled in 25.11 after security issues were resolved
      pkgs.fluffychat
      pkgs.nextcloud-talk-desktop
-      
-      # For logging back into google chat
-      globalInputs.google-cookie-retrieval.packages.${system}.default
    ];
  };
 }
--- a/home/roles/desktop/default.nix
+++ b/home/roles/desktop/default.nix
@@ -4,6 +4,7 @@ with lib;

 let
  cfg = config.home.roles.desktop;
+  isLinux = pkgs.stdenv.isLinux;
 in
 {
  options.home.roles.desktop = {
@@ -12,61 +13,63 @@ in

  config = mkIf cfg.enable {
    home.packages = with pkgs; [
-      # Desktop applications
+      # Cross-platform desktop applications
      bitwarden-desktop
-      dunst
      keepassxc
+      xdg-utils # XDG utilities for opening files/URLs with default applications
+    ] ++ optionals isLinux [
+      # Linux-only desktop applications
+      dunst
      unstable.ghostty
-      
-      # Desktop utilities
+
+      # Linux-only desktop utilities
      feh # Image viewer and wallpaper setter for X11
      rofi # Application launcher for X11
      solaar # Logitech management software
      waybar
      wofi # Application launcher for Wayland
-      xdg-utils # XDG utilities for opening files/URLs with default applications
-      
-      # System utilities with GUI components
+
+      # Linux-only system utilities with GUI components
      (snapcast.override { pulseaudioSupport = true; })
-      
-      # KDE tiling window management
+
+      # KDE tiling window management (Linux-only)
      kdePackages.krohnkite  # Dynamic tiling extension for KWin 6
-      
-      # KDE PIM applications for email, calendar, and contacts
+
+      # KDE PIM applications for email, calendar, and contacts (Linux-only)
      kdePackages.kmail
      kdePackages.kmail-account-wizard
      kdePackages.kmailtransport
      kdePackages.korganizer
      kdePackages.kaddressbook
      kdePackages.kontact
-      
-      # KDE System components needed for proper integration
+
+      # KDE System components needed for proper integration (Linux-only)
      kdePackages.kded
      kdePackages.systemsettings
      kdePackages.kmenuedit
-      
-      # Desktop menu support
+
+      # Desktop menu support (Linux-only)
      kdePackages.plasma-desktop # Contains applications.menu
-      
-      # KDE Online Accounts support
+
+      # KDE Online Accounts support (Linux-only)
      kdePackages.kaccounts-integration
      kdePackages.kaccounts-providers
      kdePackages.signond
-      
-      # KDE Mapping
+
+      # KDE Mapping (Linux-only)
      kdePackages.marble  # Virtual globe and world atlas
-      
-      # KDE Productivity
+
+      # KDE Productivity (Linux-only)
      kdePackages.kate        # Advanced text editor with syntax highlighting
      kdePackages.okular      # Universal document viewer (PDF, ePub, etc.)
      kdePackages.spectacle   # Screenshot capture utility
      kdePackages.filelight   # Visual disk usage analyzer
-      
-      # KDE Multimedia
+
+      # KDE Multimedia (Linux-only)
      kdePackages.gwenview    # Image viewer and basic editor
      kdePackages.elisa       # Music player
-      
-      # KDE System Utilities  
+
+      # KDE System Utilities (Linux-only)
      kdePackages.ark         # Archive manager (zip, tar, 7z, etc.)
      kdePackages.yakuake     # Drop-down terminal emulator
    ];
@@ -77,61 +80,66 @@ in

    programs.spotify-player.enable = true;

-    services.gnome-keyring = {
+    # Linux-only: GNOME keyring service
+    services.gnome-keyring = mkIf isLinux {
      enable = true;
    };

-    # rbw vault unlock on login and resume from suspend
-    systemd.user.services.rbw-unlock-on-login = {
-      Unit = {
-        Description = "Unlock rbw vault at login";
-        After = [ "graphical-session.target" ];
+    # Linux-only: systemd user services for rbw vault unlock
+    systemd.user.services = mkIf isLinux {
+      # rbw vault unlock on login
+      rbw-unlock-on-login = {
+        Unit = {
+          Description = "Unlock rbw vault at login";
+          After = [ "graphical-session.target" ];
+        };
+        Service = {
+          Type = "oneshot";
+          ExecStart = "${pkgs.rbw}/bin/rbw unlock";
+          Environment = "RBW_AGENT=${pkgs.rbw}/bin/rbw-agent";
+          # KillMode = "process" prevents systemd from killing the rbw-agent daemon
+          # when this oneshot service completes. The agent is spawned by rbw unlock
+          # and needs to persist after the service exits.
+          KillMode = "process";
+        };
+        Install = {
+          WantedBy = [ "graphical-session.target" ];
+        };
      };
-      Service = {
-        Type = "oneshot";
-        ExecStart = "${pkgs.rbw}/bin/rbw unlock";
-        Environment = "RBW_AGENT=${pkgs.rbw}/bin/rbw-agent";
-        # KillMode = "process" prevents systemd from killing the rbw-agent daemon
-        # when this oneshot service completes. The agent is spawned by rbw unlock
-        # and needs to persist after the service exits.
-        KillMode = "process";
-      };
-      Install = {
-        WantedBy = [ "graphical-session.target" ];
+
+      # rbw vault unlock on resume from suspend
+      rbw-unlock-on-resume = {
+        Unit = {
+          Description = "Unlock rbw vault after resume from suspend";
+          After = [ "suspend.target" ];
+        };
+        Service = {
+          Type = "oneshot";
+          ExecStart = "${pkgs.rbw}/bin/rbw unlock";
+          Environment = "RBW_AGENT=${pkgs.rbw}/bin/rbw-agent";
+          # KillMode = "process" prevents systemd from killing the rbw-agent daemon
+          # when this oneshot service completes. The agent is spawned by rbw unlock
+          # and needs to persist after the service exits.
+          KillMode = "process";
+        };
+        Install = {
+          WantedBy = [ "suspend.target" ];
+        };
      };
    };

-    systemd.user.services.rbw-unlock-on-resume = {
-      Unit = {
-        Description = "Unlock rbw vault after resume from suspend";
-        After = [ "suspend.target" ];
-      };
-      Service = {
-        Type = "oneshot";
-        ExecStart = "${pkgs.rbw}/bin/rbw unlock";
-        Environment = "RBW_AGENT=${pkgs.rbw}/bin/rbw-agent";
-        # KillMode = "process" prevents systemd from killing the rbw-agent daemon
-        # when this oneshot service completes. The agent is spawned by rbw unlock
-        # and needs to persist after the service exits.
-        KillMode = "process";
-      };
-      Install = {
-        WantedBy = [ "suspend.target" ];
-      };
-    };
-
-    # KDE environment variables for proper integration
-    home.sessionVariables = {
+    # Linux-only: KDE environment variables for proper integration
+    home.sessionVariables = mkIf isLinux {
      QT_QPA_PLATFORMTHEME = "kde";
      KDE_SESSION_VERSION = "6";
    };

    xdg = {
      enable = true;
-      
+
      # Ensure desktop files are made available for discovery
      desktopEntries = {};  # This creates the desktop files directory structure
-      
+
      mimeApps = {
        enable = true;
        associations.added = {
@@ -141,13 +149,14 @@ in
          "x-scheme-handler/https" = "firefox.desktop";
        };
        defaultApplications = {
-          # Web browsers
+          # Web browsers (cross-platform)
          "text/html" = "firefox.desktop";
          "x-scheme-handler/http" = "firefox.desktop";
          "x-scheme-handler/https" = "firefox.desktop";
          "x-scheme-handler/about" = "firefox.desktop";
          "x-scheme-handler/unknown" = "firefox.desktop";
-          
+        } // optionalAttrs isLinux {
+          # Linux-only: KDE application associations
          # Documents
          "application/pdf" = "okular.desktop";
          "text/plain" = "kate.desktop";
@@ -155,7 +164,7 @@ in
          "text/x-c" = "kate.desktop";
          "text/x-python" = "kate.desktop";
          "application/x-shellscript" = "kate.desktop";
-          
+
          # Images
          "image/png" = "gwenview.desktop";
          "image/jpeg" = "gwenview.desktop";
@@ -164,25 +173,25 @@ in
          "image/bmp" = "gwenview.desktop";
          "image/tiff" = "gwenview.desktop";
          "image/webp" = "gwenview.desktop";
-          
+
          # Archives
          "application/zip" = "ark.desktop";
          "application/x-tar" = "ark.desktop";
          "application/x-compressed-tar" = "ark.desktop";
          "application/x-7z-compressed" = "ark.desktop";
          "application/x-rar" = "ark.desktop";
-          
+
          # Audio
          "audio/mpeg" = "elisa.desktop";
          "audio/mp4" = "elisa.desktop";
          "audio/flac" = "elisa.desktop";
          "audio/ogg" = "elisa.desktop";
          "audio/wav" = "elisa.desktop";
-          
+
          # Email
          "message/rfc822" = "kmail.desktop";
          "x-scheme-handler/mailto" = "kmail.desktop";
-          
+
          # Calendar
          "text/calendar" = "korganizer.desktop";
          "application/x-vnd.akonadi.calendar.event" = "korganizer.desktop";
@@ -190,9 +199,11 @@ in
      };
    };

-    # Fix for KDE applications.menu file issue on Plasma 6
+    # Linux-only: Fix for KDE applications.menu file issue on Plasma 6
    # KDE still looks for applications.menu but Plasma 6 renamed it to plasma-applications.menu
-    xdg.configFile."menus/applications.menu".source = "${pkgs.kdePackages.plasma-workspace}/etc/xdg/menus/plasma-applications.menu";
+    xdg.configFile."menus/applications.menu" = mkIf isLinux {
+      source = "${pkgs.kdePackages.plasma-workspace}/etc/xdg/menus/plasma-applications.menu";
+    };

    # Note: modules must be imported at top-level home config
  };
--- a/home/roles/development/skills/beads_batch_research_plan.md
+++ b/home/roles/development/skills/beads_batch_research_plan.md
@@ -0,0 +1,317 @@
+---
+description: Batch research and planning for multiple beads with interactive question review
+model: opus
+---
+
+# Beads Batch Research+Plan
+
+This skill automates the common workflow of:
+1. Running /beads_research in parallel for multiple beads
+2. Presenting open questions interactively for user input (bead-by-bead)
+3. Running /beads_plan for all researched beads (plus any spawned from splits)
+
+## When to Use
+
+- You have multiple beads ready for work
+- You want to research and plan them efficiently before implementation
+- You prefer to batch your question-answering rather than context-switching between skills
+
+## Phase 1: Selection
+
+1. **Get ready beads**: Run `bd ready --limit=20` to list beads with no blockers
+
+2. **Filter already-researched beads**:
+   For each ready bead, check if it already has research:
+   ```bash
+   ls thoughts/beads-{bead-id}/research.md 2>/dev/null
+   ```
+
+   Categorize beads:
+   - **Needs research**: No `research.md` exists
+   - **Has research, needs plan**: `research.md` exists but no `plan.md`
+   - **Already planned**: Both `research.md` and `plan.md` exist
+
+3. **Present selection**:
+   ```
+   Ready beads available for batch research+plan:
+
+   NEEDS RESEARCH:
+   - {bead-id}: {title} (type: {type})
+   - ...
+
+   HAS RESEARCH (plan only):
+   - {bead-id}: {title} (type: {type})
+   - ...
+
+   ALREADY PLANNED (skip):
+   - {bead-id}: {title}
+
+   Which beads would you like to process?
+   ```
+
+4. **Use AskUserQuestion** with `multiSelect: true`:
+   - Include bead ID and title for each option
+   - Separate options by category
+   - Allow selection across categories
+
+## Phase 2: Parallel Research
+
+For each selected bead that NEEDS RESEARCH, launch a research subagent.
+
+### Subagent Instructions Template
+
+```
+Research bead [BEAD_ID]: [BEAD_TITLE]
+
+1. **Load bead context**:
+   ```bash
+   bd show [BEAD_ID]
+   ```
+
+2. **Create artifact directory**:
+   ```bash
+   mkdir -p thoughts/beads-[BEAD_ID]
+   ```
+
+3. **Conduct research** following beads_research.md patterns:
+   - Analyze and decompose the research question
+   - Spawn parallel sub-agent tasks (codebase-locator, codebase-analyzer, etc.)
+   - Synthesize findings
+
+4. **Write research document** to `thoughts/beads-[BEAD_ID]/research.md`:
+   - Include frontmatter with metadata
+   - Document findings with file:line references
+   - **CRITICAL**: Include "## Open Questions" section listing any unresolved items
+
+5. **Return summary**:
+   - Research status (complete/partial)
+   - Number of open questions
+   - Key findings summary (2-3 bullet points)
+   - List of open questions verbatim
+```
+
+### Launching Subagents
+
+Use `subagent_type: "opus"` for research subagents (matches beads_research model setting).
+
+Launch ALL research subagents in a single message for parallel execution:
+```
+<Task calls for each selected bead needing research - all in one message>
+```
+
+### Collecting Results
+
+Wait for ALL research subagents to complete. Collect:
+- Bead ID
+- Research status
+- Open questions list
+- Any errors encountered
+
+## Phase 3: Interactive Question Review
+
+Present each bead's open questions sequentially for user input.
+
+### For Each Bead (in order):
+
+1. **Present research summary**:
+   ```
+   ## Bead {N}/{total}: {bead-id} - {title}
+
+   Research complete. Key findings:
+   - {finding 1}
+   - {finding 2}
+
+   Open questions requiring your input:
+   1. {question 1}
+   2. {question 2}
+
+   Additionally:
+   - Should this bead be split into multiple beads? (y/n)
+   - If split, describe the split:
+   ```
+
+2. **Collect user responses**:
+   - Answers to open questions
+   - Split decision (yes/no)
+   - If split: new bead titles and how to divide the work
+
+3. **Handle splits**:
+   If user indicates a split:
+   ```bash
+   # Create new beads for split work
+   bd create --title="{split title 1}" --type={type} --priority={priority} \
+     --description="{description based on user input}"
+
+   # Update original bead if scope narrowed
+   bd update {original-bead-id} --description="{updated description}"
+   ```
+
+   Track new bead IDs for inclusion in planning phase.
+
+4. **Update research document**:
+   Append user answers to `thoughts/beads-{id}/research.md`:
+   ```markdown
+   ## User Clarifications [{timestamp}]
+
+   Q: {question 1}
+   A: {user answer 1}
+
+   Q: {question 2}
+   A: {user answer 2}
+
+   ## Bead Splits
+   {If split: description of split and new bead IDs}
+   ```
+
+### Progress Tracking
+
+After each bead's questions are answered, confirm before moving to next:
+```
+Questions answered for {bead-id}. {N-1} beads remaining.
+Continue to next bead? (y/n)
+```
+
+### Beads with No Questions
+
+If a bead's research had no open questions:
+```
+## Bead {N}/{total}: {bead-id} - {title}
+
+Research complete with no open questions.
+
+Key findings:
+- {finding 1}
+- {finding 2}
+
+Should this bead be split? (y/n)
+```
+
+## Phase 4: Parallel Planning
+
+After all questions answered, launch planning subagents for all beads.
+
+### Beads to Plan
+
+Include:
+- Original beads that were researched
+- Beads that had existing research (from selection phase)
+- New beads spawned from splits
+
+### Subagent Instructions Template
+
+```
+Create implementation plan for bead [BEAD_ID]: [BEAD_TITLE]
+
+1. **Load context**:
+   ```bash
+   bd show [BEAD_ID]
+   ```
+
+2. **Read research** (it exists and has user clarifications):
+   Read `thoughts/beads-[BEAD_ID]/research.md` FULLY
+
+3. **Create plan** following beads_plan.md patterns:
+   - Context gathering via sub-agents
+   - Design approach based on research findings and user clarifications
+   - **Skip interactive questions** - they were already answered in research review
+
+4. **Write plan** to `thoughts/beads-[BEAD_ID]/plan.md`:
+   - Full plan structure with phases
+   - Success criteria (automated and manual)
+   - References to research document
+
+5. **Update bead**:
+   ```bash
+   bd update [BEAD_ID] --notes="Plan created: thoughts/beads-[BEAD_ID]/plan.md"
+   ```
+
+6. **Return summary**:
+   - Plan status (complete/failed)
+   - Number of phases
+   - Estimated complexity (small/medium/large)
+   - Any issues encountered
+```
+
+### Launching Subagents
+
+Use `subagent_type: "opus"` for planning subagents (matches beads_plan model setting).
+
+Launch ALL planning subagents in a single message:
+```
+<Task calls for each bead to plan - all in one message>
+```
+
+### Handling Beads Without Research
+
+For beads that had existing research but user didn't review questions:
+- Planning subagent reads existing research
+- If research has unresolved open questions, subagent should flag this in its return
+
+## Phase 5: Summary
+
+After all planning completes, present final summary.
+
+### Summary Format
+
+```
+## Batch Research+Plan Complete
+
+### Successfully Processed:
+| Bead | Title | Research | Plan | Phases | Complexity |
+|------|-------|----------|------|--------|------------|
+| {id} | {title} | Complete | Complete | 3 | medium |
+| {id} | {title} | Complete | Complete | 2 | small |
+
+### New Beads (from splits):
+| Bead | Title | Parent | Status |
+|------|-------|--------|--------|
+| {new-id} | {title} | {parent-id} | Planned |
+
+### Failed:
+| Bead | Title | Phase Failed | Error |
+|------|-------|--------------|-------|
+| {id} | {title} | Research | Timeout |
+
+### Next Steps:
+1. Review plans at `thoughts/beads-{id}/plan.md`
+2. Run `/parallel_beads` to implement all planned beads
+3. Or run `/beads_implement {id}` for individual implementation
+
+### Artifacts Created:
+- Research: thoughts/beads-{id}/research.md (x{N} files)
+- Plans: thoughts/beads-{id}/plan.md (x{N} files)
+```
+
+## Error Handling
+
+### Research Subagent Failure
+- Log the failure with bead ID and error
+- Continue with other beads
+- Exclude failed beads from question review and planning
+- Report in final summary
+
+### Planning Subagent Failure
+- Log the failure with bead ID and error
+- Research still valid - can retry planning manually
+- Report in final summary
+
+### User Cancellation During Question Review
+- Save progress to bead notes
+- Report which beads were completed
+- User can resume with remaining beads in new session
+
+### Split Bead Creation Failure
+- Report error but continue with original bead
+- User can manually create split beads later
+
+## Resource Limits
+
+- Maximum concurrent research subagents: 5
+- Maximum concurrent planning subagents: 5
+- If more beads selected, process in batches
+
+## Notes
+
+- This skill is designed for the "research+plan before implementation" workflow
+- Pairs well with `/parallel_beads` for subsequent implementation
+- Run `/reconcile_beads` after implementation PRs merge
--- a/home/roles/development/skills/reconcile_beads.md
+++ b/home/roles/development/skills/reconcile_beads.md
@@ -4,12 +4,13 @@ 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.
+This skill reconciles beads that are in `in_review` status with their corresponding PRs. If a PR has been merged, the bead is closed and any linked Gitea issue is also 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
+- `tea` CLI must be configured for closing Gitea issues

 ## Workflow

@@ -52,6 +53,34 @@ If the PR is merged:
 bd close [BEAD_ID] --reason="PR merged: [PR_URL]"
 ```

+### Step 3.1: Close corresponding Gitea issue (if any)
+
+After closing a bead, check if it has a linked Gitea issue:
+
+1. **Check for Gitea issue URL in bead notes**:
+   Look for the pattern `Gitea issue: <URL>` in the notes. Extract the URL.
+
+2. **Extract issue number from URL**:
+   ```bash
+   # Example: https://git.johnogle.info/johno/nixos-configs/issues/16 -> 16
+   echo "$GITEA_URL" | grep -oP '/issues/\K\d+'
+   ```
+
+3. **Close the Gitea issue**:
+   ```bash
+   tea issues close [ISSUE_NUMBER]
+   ```
+
+4. **Handle errors gracefully**:
+   - If issue is already closed: Log warning, continue
+   - If issue not found: Log warning, continue
+   - If `tea` fails: Log error, continue with other beads
+
+   Example warning output:
+   ```
+   Warning: Could not close Gitea issue #16: issue already closed
+   ```
+
 ### Step 4: Report summary

 Present results:
@@ -60,10 +89,17 @@ Present results:
 ## Beads Reconciliation Summary

 ### Closed (PR Merged)
-| Bead | PR | Title |
-|------|-----|-------|
-| beads-abc | #123 | Feature X |
-| beads-xyz | #456 | Bug fix Y |
+| Bead | PR | Gitea Issue | Title |
+|------|-----|-------------|-------|
+| beads-abc | #123 | #16 closed | Feature X |
+| beads-xyz | #456 | (none) | Bug fix Y |
+
+### Gitea Issues Closed
+| Issue | Bead | Status |
+|-------|------|--------|
+| #16 | beads-abc | Closed successfully |
+| #17 | beads-def | Already closed (skipped) |
+| #99 | beads-ghi | Error: issue not found |

 ### Still in Review
 | Bead | PR | Status | Title |
@@ -80,9 +116,14 @@ Present results:
 - **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
+- **Gitea issue already closed**: Log warning, continue (not an error)
+- **Gitea issue not found**: Log warning, continue (issue may have been deleted)
+- **No Gitea issue linked**: Normal case, no action needed
+- **tea command fails**: Log error with output, continue with other beads

 ## 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
+- Gitea issues are only closed for beads that have a `Gitea issue: <URL>` in their notes
--- a/home/roles/emacs/doom/config.el
+++ b/home/roles/emacs/doom/config.el
@@ -225,11 +225,16 @@
        mu4e-headers-time-format "%H:%M")

  ;; Sending mail via msmtp
-  (setq message-send-mail-function 'message-send-mail-with-sendmail
-        sendmail-program (executable-find "msmtp")
-        message-sendmail-envelope-from 'header
-        mail-envelope-from 'header
-        mail-specify-envelope-from t))
+  ;; NOTE: message-sendmail-f-is-evil and --read-envelope-from are required
+  ;; to prevent msmtp from stripping the email body when processing headers.
+  ;; Without these, multipart messages (especially from org-msg) may arrive
+  ;; with empty bodies.
+  (setq sendmail-program (executable-find "msmtp")
+        send-mail-function #'message-send-mail-with-sendmail
+        message-send-mail-function #'message-send-mail-with-sendmail
+        message-sendmail-f-is-evil t
+        message-sendmail-extra-arguments '("--read-envelope-from")
+        message-sendmail-envelope-from 'header))

 ;; Whenever you reconfigure a package, make sure to wrap your config in an
 ;; `after!' block, otherwise Doom's defaults may override your settings. E.g.
--- a/home/roles/email/default.nix
+++ b/home/roles/email/default.nix
@@ -4,6 +4,7 @@ with lib;

 let
  cfg = config.home.roles.email;
+  isLinux = pkgs.stdenv.isLinux;
 in
 {
  options.home.roles.email = {
@@ -89,34 +90,38 @@ in
      account default : proton
    '';

-    # Systemd service for mail sync
-    systemd.user.services.mbsync = {
-      Unit = {
-        Description = "Mailbox synchronization service";
-        After = [ "network-online.target" ];
-        Wants = [ "network-online.target" ];
-      };
-      Service = {
-        Type = "oneshot";
-        ExecStart = "${pkgs.bash}/bin/bash -c 'mkdir -p ~/Mail && ${pkgs.isync}/bin/mbsync -a && (${pkgs.mu}/bin/mu info >/dev/null 2>&1 || ${pkgs.mu}/bin/mu init --maildir ~/Mail --personal-address=john@ogle.fyi) && ${pkgs.mu}/bin/mu index'";
-        Environment = "PATH=${pkgs.rbw}/bin:${pkgs.coreutils}/bin";
-        StandardOutput = "journal";
-        StandardError = "journal";
+    # Linux-only: Systemd service for mail sync (Darwin uses launchd instead)
+    systemd.user.services = mkIf isLinux {
+      mbsync = {
+        Unit = {
+          Description = "Mailbox synchronization service";
+          After = [ "network-online.target" ];
+          Wants = [ "network-online.target" ];
+        };
+        Service = {
+          Type = "oneshot";
+          ExecStart = "${pkgs.bash}/bin/bash -c 'mkdir -p ~/Mail && ${pkgs.isync}/bin/mbsync -a && (${pkgs.mu}/bin/mu info >/dev/null 2>&1 || ${pkgs.mu}/bin/mu init --maildir ~/Mail --personal-address=john@ogle.fyi) && ${pkgs.mu}/bin/mu index'";
+          Environment = "PATH=${pkgs.rbw}/bin:${pkgs.coreutils}/bin";
+          StandardOutput = "journal";
+          StandardError = "journal";
+        };
      };
    };

-    # Systemd timer for automatic sync
-    systemd.user.timers.mbsync = {
-      Unit = {
-        Description = "Mailbox synchronization timer";
-      };
-      Timer = {
-        OnBootSec = "2min";
-        OnUnitActiveSec = "5min";
-        Unit = "mbsync.service";
-      };
-      Install = {
-        WantedBy = [ "timers.target" ];
+    # Linux-only: Systemd timer for automatic sync
+    systemd.user.timers = mkIf isLinux {
+      mbsync = {
+        Unit = {
+          Description = "Mailbox synchronization timer";
+        };
+        Timer = {
+          OnBootSec = "2min";
+          OnUnitActiveSec = "5min";
+          Unit = "mbsync.service";
+        };
+        Install = {
+          WantedBy = [ "timers.target" ];
+        };
      };
    };
  };
--- a/home/roles/kdeconnect/default.nix
+++ b/home/roles/kdeconnect/default.nix
@@ -4,13 +4,15 @@ with lib;

 let
  cfg = config.home.roles.kdeconnect;
+  isLinux = pkgs.stdenv.isLinux;
 in
 {
  options.home.roles.kdeconnect = {
    enable = mkEnableOption "Enable KDE Connect for device integration";
  };

-  config = mkIf cfg.enable {
+  # KDE Connect services are Linux-only (requires D-Bus and systemd)
+  config = mkIf (cfg.enable && isLinux) {
    services.kdeconnect = {
      enable = true;
      indicator = true;
--- a/home/roles/sync/default.nix
+++ b/home/roles/sync/default.nix
@@ -4,6 +4,7 @@ with lib;

 let
  cfg = config.home.roles.sync;
+  isLinux = pkgs.stdenv.isLinux;
 in
 {
  options.home.roles.sync = {
@@ -11,9 +12,10 @@ in
  };

  config = mkIf cfg.enable {
-    home.packages = with pkgs; [
+    # Linux-only: syncthingtray requires system tray support
+    home.packages = optionals isLinux (with pkgs; [
      syncthingtray
-    ];
+    ]);

    services.syncthing = {
      enable = true;
--- a/machines/wixos/configuration.nix
+++ b/machines/wixos/configuration.nix
@@ -1,56 +0,0 @@
-# Edit this configuration file to define what should be installed on
-# your system. Help is available in the configuration.nix(5) man page, on
-# https://search.nixos.org/options and in the NixOS manual (`nixos-help`).
-
-# NixOS-WSL specific options are documented on the NixOS-WSL repository:
-# https://github.com/nix-community/NixOS-WSL
-
-{ config, lib, pkgs, ... }:
-
-{
-  imports = [
-  ];
-
-  roles = {
-    audio.enable = true;
-    desktop = {
-      enable = true;
-      wayland = true;
-    };
-    nvidia = {
-      enable = true;
-      package = "latest";
-      graphics.extraPackages = with pkgs; [
-        mesa
-        libvdpau-va-gl
-        libva-vdpau-driver
-      ];
-    };
-    users.enable = true;
-  };
-
-  networking.hostName = "wixos";
-
-  wsl.enable = true;
-  wsl.defaultUser = "johno";
-  wsl.startMenuLaunchers = true;
-  wsl.useWindowsDriver = true;
-  wsl.wslConf.network.hostname = "wixos";
-  wsl.wslConf.user.default = "johno";
-
-  # WSL-specific environment variables for graphics
-  environment.sessionVariables = {
-    LD_LIBRARY_PATH = [
-      "/usr/lib/wsl/lib"
-      "/run/opengl-driver/lib"
-    ];
-  };
-
-  # This value determines the NixOS release from which the default
-  # settings for stateful data, like file locations and database versions
-  # on your system were taken. It's perfectly fine and recommended to leave
-  # this value at the release version of the first install of this system.
-  # Before changing this value read the documentation for this option
-  # (e.g. man configuration.nix or on https://nixos.org/nixos/options.html).
-  system.stateVersion = "24.05"; # Did you read the comment?
-}
--- a/roles/audio/default.nix
+++ b/roles/audio/default.nix
@@ -21,6 +21,8 @@ in

      services.pipewire = {
        enable = true;
+        alsa.enable = true;
+        alsa.support32Bit = true;
        pulse.enable = true;
      };

--- a/scripts/rotate-wallpaper.sh
+++ b/scripts/rotate-wallpaper.sh
@@ -1,6 +1,30 @@
 #!/usr/bin/env bash
 set -euo pipefail

+# Parse arguments
+while [[ $# -gt 0 ]]; do
+    case $1 in
+        --help|-h)
+            echo "Usage: $0 [OPTIONS]"
+            echo ""
+            echo "Rotate to the next wallpaper in the configured list."
+            echo ""
+            echo "This script increments the currentIndex in home/wallpapers/default.nix,"
+            echo "cycling through available wallpapers. Rebuild your system to apply"
+            echo "the new wallpaper."
+            echo ""
+            echo "Options:"
+            echo "  --help, -h    Show this help message"
+            exit 0
+            ;;
+        *)
+            echo "Unknown option: $1"
+            echo "Use --help for usage information"
+            exit 1
+            ;;
+    esac
+done
+
 # Colors for output
 RED='\033[0;31m'
 GREEN='\033[0;32m'
--- a/scripts/update-doomemacs.sh
+++ b/scripts/update-doomemacs.sh
@@ -1,6 +1,30 @@
 #!/usr/bin/env bash
 set -euo pipefail

+# Parse arguments
+while [[ $# -gt 0 ]]; do
+    case $1 in
+        --help|-h)
+            echo "Usage: $0 [OPTIONS]"
+            echo ""
+            echo "Update Doom Emacs to the latest commit from the doomemacs repository."
+            echo ""
+            echo "This script fetches the latest commit SHA from the default branch,"
+            echo "updates the rev and sha256 in home/roles/emacs/default.nix, and"
+            echo "prepares the configuration for a system rebuild."
+            echo ""
+            echo "Options:"
+            echo "  --help, -h    Show this help message"
+            exit 0
+            ;;
+        *)
+            echo "Unknown option: $1"
+            echo "Use --help for usage information"
+            exit 1
+            ;;
+    esac
+done
+
 # Colors for output
 RED='\033[0;31m'
 GREEN='\033[0;32m'
--- a/scripts/upgrade.sh
+++ b/scripts/upgrade.sh
@@ -1,6 +1,35 @@
 #!/usr/bin/env bash
 set -euo pipefail

+# Parse arguments
+while [[ $# -gt 0 ]]; do
+    case $1 in
+        --help|-h)
+            echo "Usage: $0 [OPTIONS]"
+            echo ""
+            echo "Perform a major upgrade of the NixOS configuration."
+            echo ""
+            echo "This script runs the following steps:"
+            echo "  1. Update all flake inputs (nix flake update)"
+            echo "  2. Update Doom Emacs to the latest commit"
+            echo "  3. Update Claude Code to the latest version"
+            echo "  4. Rotate to the next wallpaper"
+            echo ""
+            echo "After completion, review changes with 'git diff' and rebuild"
+            echo "your system with 'sudo nixos-rebuild switch --flake .'"
+            echo ""
+            echo "Options:"
+            echo "  --help, -h    Show this help message"
+            exit 0
+            ;;
+        *)
+            echo "Unknown option: $1"
+            echo "Use --help for usage information"
+            exit 1
+            ;;
+    esac
+done
+
 # Colors for output
 RED='\033[0;31m'
 GREEN='\033[0;32m'
Author	SHA1	Message	Date
John Ogle	ec47c4bb4f	feat(skills): Add batch research+plan skill for multiple beads All checks were successful CI / check (pull_request) Successful in 3m4s Details	2026-01-14 14:00:30 -08:00
John Ogle	667f5b28dc	feat(skills): Close Gitea issues when beads are reconciled Some checks failed CI / check (push) Has been cancelled Details	2026-01-14 13:59:30 -08:00
John Ogle	4bb71d0b7e	Remove wixos (WSL) configuration All checks were successful CI / check (push) Successful in 3m0s Details WSL is no longer used. This removes: - machines/wixos/ directory and configuration.nix - nixos-wsl input from flake.nix - nixosConfigurations.wixos output - References to wixos in AGENTS.md and .goosehints Implements bead: nixos-configs-2mk	2026-01-13 18:02:36 -08:00
John Ogle	0bc134f557	fix(mu4e): Configure msmtp to preserve email body content All checks were successful CI / check (push) Successful in 6m0s Details The mu4e msmtp configuration was causing email bodies to be stripped, especially for multipart messages from org-msg. This was due to missing critical msmtp settings. Changes: - Add message-sendmail-f-is-evil to prevent -f flag issues - Add --read-envelope-from to msmtp arguments - Set both send-mail-function and message-send-mail-function Fixes: nixos-configs-9l8	2026-01-13 17:48:36 -08:00
John Ogle	1b9df3926e	Fix conflicting audio role config: remove pulseaudio, keep pipewire Some checks failed CI / check (push) Has been cancelled Details Remove services.pulseaudio configuration that conflicted with services.pipewire. PipeWire replaces PulseAudio and provides compatibility through pulse.enable. Also added alsa.enable and alsa.support32Bit for better ALSA support.	2026-01-13 17:48:00 -08:00
John Ogle	bd98793528	feat(roles): Parameterize hardcoded values in printing, nfs-mounts, and virtualisation roles Some checks failed CI / check (push) Has been cancelled Details - printing role: Add configurable printerName, printerUri, and printerModel options to replace hardcoded Brother printer values - nfs-mounts role: Add configurable server, remotePath, and mountPoint options to replace hardcoded NFS server IP (10.0.0.43) - virtualisation role: Add configurable dockerUsers option as list type to replace hardcoded 'johno' docker group membership All options have sensible defaults matching the original hardcoded values, ensuring backward compatibility while allowing per-host customization. Implements bead: nixos-configs-fkt	2026-01-13 17:20:59 -08:00
John Ogle	d78637cf13	feat(home-manager): Add platform compatibility guards to cross-platform roles Some checks failed CI / check (push) Has been cancelled Details Add lib.optionals pkgs.stdenv.isLinux guards to roles that contain Linux-only packages or services to prevent build failures on Darwin: - communication: Guard Electron apps (element-desktop, fluffychat, nextcloud-talk-desktop) that don't build on Darwin due to electron build-from-source limitations - kdeconnect: Guard entire config block since services.kdeconnect requires D-Bus and systemd (Linux-only) - sync: Guard syncthingtray package (requires Linux system tray) - email: Guard systemd.user.services/timers (Darwin uses launchd) - desktop: Guard Linux-only packages, services, and KDE-specific configurations including gnome-keyring, systemd services, and XDG mime associations Implements bead: nixos-configs-tcu	2026-01-13 17:20:01 -08:00
John Ogle	08d16bd2c9	feat(scripts): Add --help flags to all flake apps Some checks failed CI / check (push) Has been cancelled Details Add consistent --help/-h argument handling to update-doomemacs.sh, rotate-wallpaper.sh, and upgrade.sh scripts. Each script now displays usage information and a description of what it does. update-claude-code already had --help support.	2026-01-13 17:18:46 -08:00
John Ogle	a14ff9be4d	fix(flake): Remove duplicate home-manager imports from wixos and zix790prors Some checks failed CI / check (pull_request) Successful in 5m36s Details CI / check (push) Has been cancelled Details The nixosModules list already includes inputs.home-manager.nixosModules.home-manager, so these individual configuration imports were redundant.	2026-01-13 16:37:41 -08:00