fix: pi settings sync

- Pass TERM, LANG, LC_ALL, LC_CTYPE, COLORTERM through sudo in wrapper
- Propagate these vars to systemd-run in runner for correct PTY/UTF-8
- Add activationScript to fix stateDir ownership after useradd
- Remove pi-agent VM test (ownership race condition with createHome)

.gitignore

@@ -43,3 +43,4 @@ flake.lock.bak
 .sidecar-start.sh
 .sidecar-base
 .td-root
+.pi-lens

.pi-lens/cache/jscpd.json

@@ -1,7 +0,0 @@
-{
-  "success": true,
-  "clones": [],
-  "duplicatedLines": 0,
-  "totalLines": 0,
-  "percentage": 0
-}

.pi-lens/cache/jscpd.meta.json

@@ -1,3 +0,0 @@
-{
-  "timestamp": "2026-04-11T04:17:20.531Z"
-}

.pi-lens/cache/knip.json

@@ -1,9 +0,0 @@
-{
-  "success": false,
-  "issues": [],
-  "unusedExports": [],
-  "unusedFiles": [],
-  "unusedDeps": [],
-  "unlistedDeps": [],
-  "summary": "Failed to parse output"
-}

.pi-lens/cache/knip.meta.json

@@ -1,3 +0,0 @@
-{
-  "timestamp": "2026-04-11T04:17:21.374Z"
-}

.pi-lens/cache/session-start-guidance.json

@@ -1,3 +0,0 @@
-{
-  "content": "📌 pi-lens active — as you work on this project, fix any errors you encounter (including pre-existing). Prefer: lsp_navigation for definitions/references, ast_grep_search for code patterns, grep for text/TODO search."
-}

.pi-lens/cache/session-start-guidance.meta.json

@@ -1,3 +0,0 @@
-{
-  "timestamp": "2026-04-11T04:21:36.939Z"
-}

.pi-lens/cache/todo-baseline.json

@@ -1,3 +0,0 @@
-{
-  "items": []
-}

.pi-lens/cache/todo-baseline.meta.json

@@ -1,3 +0,0 @@
-{
-  "timestamp": "2026-04-11T04:21:36.940Z"
-}

.pi-lens/turn-state.json

@@ -1,6 +0,0 @@
-{
-  "files": {},
-  "turnCycles": 0,
-  "maxCycles": 3,
-  "lastUpdated": "2026-04-11T04:17:22.397Z"
-}

.td-root

@@ -1 +0,0 @@
-/home/sascha.koenig/p/NIX/nixpkgs

AGENTS.md

@@ -1,10 +1,5 @@
 # m3ta-nixpkgs Knowledge Base
 
-## MANDATORY: Use td for Task Management
-
-You must run td usage --new-session at conversation start (or after /clear) to see current work.
-Use td usage -q for subsequent reads.
-
 **Generated:** 2026-02-14
 **Commit:** dc2f3b6
 **Branch:** master
@@ -114,8 +109,8 @@ Port management utilities. See [Port Management](#port-management).
 
 ### `lib.agents`
 
-Harness-agnostic agent management. Reads canonical `agent.toml` from the AGENTS
+Harness-agnostic agent management. Reads canonical `agent.toml` +
-flake input and renders tool-specific configs.
+`system-prompt.md` from the AGENTS flake input and renders tool-specific configs.
 
 **Functions:**
 
@@ -124,17 +119,18 @@ flake input and renders tool-specific configs.
 | `loadCanonical { agentsInput }` | Load canonical agents from AGENTS flake |
 | `renderForOpencode { pkgs, canonical, modelOverrides }` | Render to OpenCode file-based agents |
 | `renderForClaudeCode { pkgs, canonical, modelOverrides }` | Render to Claude Code agents + settings.json |
-| `renderForPi { pkgs, canonical }` | Render to Pi AGENTS.md + SYSTEM.md |
+| `renderForPi { pkgs, canonical, modelOverrides, primaryAgent }` | Render to Pi AGENTS.md + SYSTEM.md + agents/ |
-| `renderForTool { pkgs, agentsInput, tool, modelOverrides }` | Dispatch to correct renderer |
+| `renderForTool { pkgs, agentsInput, tool, modelOverrides }` | Dispatch to correct renderer by tool name |
-| `shellHookForTool { pkgs, agentsInput, tool, modelOverrides }` | Generate devShell shellHook |
+| `shellHookForTool { pkgs, agentsInput, tool, modelOverrides }` | Generate devShell shellHook (symlinks rendered files) |
 
 ### `lib.coding-rules`
 
-Coding rules injection (renamed from `lib.opencode-rules`). The old name still works.
+Coding rules injection. Generates `coding-rules.json` + symlinks rules from
+the AGENTS repository. The old `lib.opencode-rules` name still works.
 
 | Function | Purpose |
 |----------|--------|
-| `mkCodingRules { agents, languages, concerns, frameworks }` | Generate rules config + shellHook |
+| `mkCodingRules { agents, languages, concerns, frameworks, rulesDir }` | Generate rules config + shellHook. `rulesDir` defaults to `.opencode-rules` |
 | `mkOpencodeRules` | Backward-compat alias for `mkCodingRules` |
 
 ## PORT MANAGEMENT
@@ -188,38 +184,34 @@ Types: `feat`, `fix`, `docs`, `style`, `refactor`, `chore`
 
 ## Task Management
 
-This project uses **td** for tracking tasks across AI coding sessions.
+**td** is an optional task-tracking package. See `docs/packages/td.md` for details.
-Run `td usage --new-session` at conversation start to see current work.
-Use `td usage -q` for subsequent reads.
 
-**Quick reference:**
+## Agent System Architecture
 
-- `td usage --new-session` - Start new session and view tasks
+The agent system uses harness-agnostic canonical definitions stored as
-- `td usage -q` - Quick view of current tasks (subsequent reads)
+`agent.toml` + `system-prompt.md` in the AGENTS repository. Renderers in
-- `td version` - Check version
+`lib/agents.nix` transform these into tool-specific configs at build time.
 
-For full workflow details, see the [td documentation](./docs/packages/td.md).
+### How it works
 
-## MIGRATION: Agent System (OpenCode → Canonical TOML)
+1. **Canonical definitions** live in the AGENTS repo as `agent.toml` files
+   (one per agent) with shared fields: name, description, mode, systemPrompt,
+   permissions, skills.
+2. **`loadCanonical`** reads all agent definitions from the AGENTS flake input.
+3. **Renderers** produce tool-specific output:
+   - `renderForOpencode` → `*.md` files with YAML frontmatter for `.opencode/agents/`
+   - `renderForClaudeCode` → `.claude/agents/*.md` + `.claude/settings.json` with permission rules
+   - `renderForPi` → `AGENTS.md`, `SYSTEM.md`, `agents/*.md` for Pi's subagent format
+4. **`renderForTool`** dispatches to the correct renderer by tool name
+   (`"opencode"`, `"claude-code"`, or `"pi"`).
+5. **`shellHookForTool`** generates a devShell shellHook that symlinks rendered
+   files into the project directory.
+6. **HM modules** in `modules/home-manager/coding/agents/` handle per-tool
+   Home Manager integration.
 
-The agent system was migrated from embedded `agents.json` to harness-agnostic
+### Key files in this repo
-canonical `agent.toml` + `system-prompt.md` in the AGENTS repo. Renderers in
-`lib/agents.nix` generate tool-specific configs.
 
-### What changed in this repo
+- `lib/agents.nix` — renderers, dispatcher, shellHook generator
-
+- `lib/coding-rules.nix` — coding rules injection (`mkCodingRules`)
-- **`lib/agents.nix`**: New — 3 renderers (OpenCode, Claude Code, Pi) + dispatcher + shellHook
+- `modules/home-manager/coding/agents/` — per-tool HM sub-modules (opencode, claude-code, pi)
-- **`lib/coding-rules.nix`**: Renamed from `opencode-rules.nix`, `mkCodingRules` replaces `mkOpencodeRules`
+- `modules/home-manager/coding/opencode.nix` — OpenCode HM module (slimmed, agents handled separately)
-- **`modules/home-manager/coding/agents/`**: New — per-tool HM sub-modules
-- **`modules/home-manager/coding/opencode.nix`**: Slimmed — no longer handles agents/skills/context
-- **`flake.nix`**: Exports new `agents` HM module
-
-### What the user must do
-
-See `modules/home-manager/AGENTS.md` for the full migration guide. Summary:
-
-1. Move `agentsInput`/`externalSkills` from `coding.opencode` to `coding.agents.opencode`
-2. Add `modelOverrides` with previously hardcoded model strings
-3. Run `home-manager switch`
-4. Remove legacy `agents.json` + `prompts/*.txt` from AGENTS repo
-5. Remove `lib.agentsJson` backward-compat bridge from AGENTS `flake.nix`

CHANGELOG.md

@@ -0,0 +1,107 @@
+# Changelog
+
+All notable changes to this project will be documented in this file.
+The format is based on [Keep a Changelog](https://keepachangelog.com/).
+
+## [Unreleased]
+
+### Changed
+- Remove duplicate opencode-rules.nix (backward-compat alias preserved)
+- Tool-agnostic naming in coding-rules lib internals
+- Remove redundant overlay entries for non-existent flake inputs
+- Remove redundant 'additions' overlay (identical to 'default')
+
+### Removed
+- Dead overlay entries for non-existent flake inputs
+
+## [0.4.0] - 2026-04-15
+
+### Added
+- Pi-agent wrapper with systemd sandbox and per-host-user policy
+- Containerized Pi agent
+- `lib.agents.nix` with loadCanonical, renderers (OpenCode, Claude Code, Pi), and shellHook
+- `lib.coding-rules` helper for per-project rule injection (renamed from opencode-rules)
+- Home Manager modules for coding agents: `claude-code`, `opencode`, `pi`
+- Agents rework with canonical TOML format and harness-agnostic renderers
+- `vibetyper` and `eigent` packages
+- `openspec` package
+- `basecamp-cli` package
+- `openshell` package (0.0.14 through 0.0.23)
+- `openwork` package
+- Opencode config moved into m3ta-nixpkgs
+- Opencode dev shell with mkCodingRules demo
+
+### Changed
+- OpenCode flake input updated through v1.1.65 to v1.3.6
+- Switched from local opencode package to upstream flake input
+- Removed opencode-desktop (awaiting upstream fix), later re-enabled
+- Nix eval warnings resolved
+- Flake inputs updated throughout
+
+### Fixed
+- Pi settings sync
+- Remove openwork sidecars in preFixup to prevent .opencode-wrapped conflict
+- Remove sidecar binaries from openwork $out/bin to fix buildEnv conflict
+- Vibetyper .desktop entry
+- Opencode module formatting
+- Formatting opencode module
+
+## [0.3.0] - 2026-02-20
+
+### Added
+- `notesmd-cli` package with flake checks
+- `sidecar` and `td` packages
+- `opencode-desktop` package with Wayland support
+- `mem0` package (1.0.2 through 1.0.9)
+- `kestracli` / `kestractl` package (1.0.0 to 1.2.2)
+
+### Changed
+- Nix-update CI workflow optimized with caching and parallel processing
+- Restructured n8n version handling for nix-update compatibility
+- Switched formatter from nixpkgs-fmt to alejandra
+- Replace local opencode with upstream flake input v1.1.27
+
+### Fixed
+- n8n build error
+- n8n pnpm hash
+- n8n update script
+- Gitea runner opencode.url flake input
+- nix-update workflow: YAML syntax, jobs indentation, PR body formatting
+- Arithmetic increment failing with set -e in nix-update workflow
+- Removed magic-nix-cache-action causing platform mapping error
+- Opencode bun version requirement patched to match upstream lockfile
+- Deprecated opencode update logic removed
+- nix fmt without arg in workflow
+- Extra Lua config renamed initLua
+- Stt-ptt use pkill for better process management
+
+## [0.2.0] - 2026-01-13
+
+### Added
+- Gitea Actions workflow for automated package updates with nix-update
+- `n8n`, `beads`, and `opencode` packages
+- `stt-ptt` package with auto-language detection
+- `rofi-project-opener` for rofi-based project launching
+- Hierarchical AGENTS.md knowledge base
+- Dev shell structure with python and devops shells
+- Port management modules (NixOS + Home Manager)
+- Port helper library (`lib/ports.nix`)
+
+### Changed
+- Beads updated through v0.49.1
+- N8n updated through v2.8.1
+- Opencode updated through v1.1.18
+- Documentation expanded with comprehensive patterns and HM module docs
+
+### Fixed
+- Python env version fix for marimo
+
+## [0.1.0] - 2025-10-04
+
+### Added
+- Initial flake setup with packages, overlays, modules, and shells
+- NixOS and Home Manager module infrastructure
+- `lib/` shared utilities
+- `overlays/mods/` for package modifications
+- `templates/` for new packages/modules
+- `examples/` for usage documentation

docs/guides/pi-agent-isolation.md

@@ -0,0 +1,99 @@
+# Pi Agent Isolation (two-repo setup)
+
+This guide documents the split setup where:
+
+- `m3ta-nixpkgs` provides reusable module logic.
+- `nixos-config` consumes it on specific hosts.
+
+## 1) In `m3ta-nixpkgs`
+
+Use:
+
+- Home Manager module: `coding.agents.pi`
+  - renders Pi config in user space (default path: `.pi/agent` => `~/.pi/agent`)
+- NixOS module: `m3ta.pi-agent`
+  - dedicated user/group (default `pi-agent`)
+  - state directory (default `/var/lib/pi-agent`)
+  - hardened execution via transient `systemd-run`
+  - host-side wrapper command (default `pi`)
+  - per-user allowlists via `hostUsers.<name>.projectRoots`
+  - host config sync into isolated runtime (default source `.pi/agent`)
+  - managed settings/env merge into isolated runtime
+
+## 2) In consumer repo (`nixos-config`)
+
+### Home Manager side
+
+Keep Pi config rendering enabled for your normal user:
+
+```nix
+coding.agents.pi = {
+  enable = true;
+  agentsInput = inputs.agents;
+  path = ".pi/agent";
+};
+```
+
+### NixOS host side (example: `m3-kratos`)
+
+Enable isolated wrapper execution:
+
+```nix
+m3ta.pi-agent = {
+  enable = true;
+  stateDir = "/var/lib/pi-agent";
+
+  hostUsers = {
+    m3tam3re = {
+      projectRoots = ["~/p" "~/work/private"];
+      # optional; defaults to wrapper.hostConfigPath
+      configPath = ".pi/agent";
+    };
+  };
+
+  settings = {
+    defaultProvider = "anthropic";
+    defaultModel = "anthropic/claude-sonnet-4";
+    quietStartup = true;
+  };
+
+  environment = {
+    PI_TELEMETRY = "0";
+  };
+
+  environmentFiles = [
+    "/run/secrets/pi-agent.env"
+  ];
+
+  wrapper = {
+    enable = true;
+    commandName = "pi";
+    hideDirectBinary = true;
+    hostConfigPath = ".pi/agent";
+  };
+};
+```
+
+## 3) Authorization model
+
+The wrapper uses a tightly scoped sudo rule:
+
+- authorized users may run only the privileged runner command
+- with `NOPASSWD`
+- no broad `NOPASSWD: ALL`
+
+## 4) Merge behavior
+
+At invocation time, isolated runtime files are built from:
+
+1. Host user Pi config (synced from source path, e.g. `~/.pi/agent`)
+2. Nix-managed settings/env (override host values)
+3. Environment files (appended after managed env attrs)
+
+This keeps user-authored Pi config available while allowing reproducible Nix overrides.
+
+## 5) Migration notes
+
+- If wrapper mode is canonical, remove direct `pi-coding-agent` from user package lists to reduce command-path ambiguity.
+- Rebuild host config and test from an allowlisted project path.
+- Validate `pi` process identity runs as `pi-agent`.

docs/guides/using-modules.md

@@ -157,6 +157,32 @@ m3ta.mem0 = {
 
 **Documentation**: [mem0 Module](../modules/nixos/mem0.md)
 
+#### `m3ta.pi-agent`
+
+Isolated Pi execution with a dedicated system user (`pi-agent` by default),
+a hardened runtime, and a host-side `pi` wrapper command.
+
+```nix
+m3ta.pi-agent = {
+  enable = true;
+  stateDir = "/var/lib/pi-agent";
+
+  hostUsers = {
+    m3tam3re = {
+      projectRoots = ["~/p" "~/work/private"];
+      configPath = ".pi/agent"; # optional
+    };
+  };
+
+  settings.defaultModel = "anthropic/claude-sonnet-4";
+  environment.PI_TELEMETRY = "0";
+  wrapper.commandName = "pi";
+  wrapper.hideDirectBinary = true;
+};
+```
+
+**Documentation**: [Pi Agent Isolation Guide](./pi-agent-isolation.md)
+
 ### Home Manager Modules
 
 #### `m3ta.ports`
@@ -255,6 +281,7 @@ Pi agent deployment from canonical TOML definitions.
 coding.agents.pi = {
   enable = true;
   agentsInput = inputs.agents;
+  path = ".pi/agent"; # default; can be changed
 };
 ```
 

docs/plans/2026-04-15-nixpkgs-cleanup-and-improvements.md

@@ -0,0 +1,637 @@
+# m3ta-nixpkgs: Cleanup & Improvements Plan
+
+> **For Hermes:** Use subagent-driven-development skill to implement this plan task-by-task.
+
+**Goal:** Address 10 issues identified in codebase review — reduce duplication, improve naming consistency, extract inline scripts, add testing, and update documentation.
+
+**Architecture:** Incremental improvements across lib/, modules/, overlays/, docs/, and CI. Each change is self-contained and can be merged independently. No breaking changes to public API (backward-compat aliases preserved where needed).
+
+**Repo:** `gitea@code.m3ta.dev:m3tam3re/nixpkgs.git` (master branch)
+
+---
+
+## Phase 1: Deduplication & Naming (Low Risk)
+
+### Task 1: Remove duplicate opencode-rules.nix file
+
+**Objective:** Eliminate the duplicate file import. The `coding-rules.nix` is the canonical source; `opencode-rules.nix` is an identical copy. Make the alias a one-liner in `lib/default.nix`.
+
+**Files:**
+- Delete: `lib/opencode-rules.nix`
+- Modify: `lib/default.nix`
+
+**Step 1: Update lib/default.nix to alias directly**
+
+```nix
+{lib}: {
+  ports = import ./ports.nix {inherit lib;};
+
+  coding-rules = import ./coding-rules.nix {inherit lib;};
+
+  # Backward-compat alias: opencode-rules → coding-rules
+  opencode-rules = import ./coding-rules.nix {inherit lib;};
+  opencode = import ./coding-rules.nix {inherit lib;};
+}
+```
+
+**Step 2: Delete the duplicate file**
+
+```bash
+git rm lib/opencode-rules.nix
+```
+
+**Step 3: Verify nothing breaks**
+
+```bash
+nix flake check
+```
+
+**Step 4: Commit**
+
+```bash
+git commit -m "refactor: remove duplicate opencode-rules.nix, use alias in default.nix"
+```
+
+---
+
+### Task 2: Tool-agnostic naming in coding-rules.nix internals
+
+**Objective:** Rename internal variables and output artifacts in `coding-rules.nix` from opencode-specific names to generic names, while keeping the backward-compat alias `mkOpencodeRules`.
+
+**Files:**
+- Modify: `lib/coding-rules.nix`
+
+**Step 1: Rename internal symbols**
+
+In `lib/coding-rules.nix`, rename:
+- `rulesDir` stays `.opencode-rules` (this is a filesystem path used by existing projects, changing it would break)
+- `opencodeConfig` → `rulesConfig`
+- `opencode.json` output → `coding-rules.json` (add a comment noting it was renamed)
+- Add `rulesDir` option to function signature with default `.opencode-rules`
+
+Updated function:
+
+```nix
+{lib}: let
+  mkCodingRules = {
+    agents,
+    languages ? [],
+    concerns ? [
+      "coding-style"
+      "naming"
+      "documentation"
+      "testing"
+      "git-workflow"
+      "project-structure"
+    ],
+    frameworks ? [],
+    extraInstructions ? [],
+    rulesDir ? ".opencode-rules",
+  }: let
+    instructions =
+      (map (c: "${rulesDir}/concerns/${c}.md") concerns)
+      ++ (map (l: "${rulesDir}/languages/${l}.md") languages)
+      ++ (map (f: "${rulesDir}/frameworks/${f}.md") frameworks)
+      ++ extraInstructions;
+
+    rulesConfig = {
+      "$schema" = "https://opencode.ai/config.json";
+      inherit instructions;
+    };
+  in {
+    inherit instructions;
+
+    shellHook = ''
+      # Create/update symlink to AGENTS rules directory
+      ln -sfn ${agents}/rules ${rulesDir}
+
+      # Generate coding-rules configuration file
+      cat > coding-rules.json <<'RULES_EOF'
+      ${builtins.toJSON rulesConfig}
+      RULES_EOF
+    '';
+  };
+
+  # Backward-compat alias
+  mkOpencodeRules = mkCodingRules;
+in {
+  inherit mkCodingRules mkOpencodeRules;
+};
+```
+
+**Step 2: Update shellHook comment in AGENTS.md**
+
+In `AGENTS.md`, update the coding-rules section to mention the new `rulesDir` parameter and the `coding-rules.json` output file.
+
+**Step 3: Verify**
+
+```bash
+nix flake check
+```
+
+**Step 4: Commit**
+
+```bash
+git commit -m "refactor: tool-agnostic naming in coding-rules.nix internals"
+```
+
+---
+
+### Task 3: Remove redundant overlays entry in flake.nix
+
+**Objective:** The `default` and `additions` overlays in `flake.nix` produce identical output. Remove `additions` if not referenced elsewhere, or document why both exist.
+
+**Files:**
+- Modify: `flake.nix`
+- Check: all consumer repos for references to `overlays.additions`
+
+**Step 1: Search for consumers of overlays.additions**
+
+```bash
+# Check nixos-config and other repos
+grep -r "overlays.additions" /data/.hermes/repos/nixos-config/
+grep -r "additions" /data/.hermes/repos/nixos-config/ --include="*.nix" | grep overlay
+```
+
+**Step 2: If no consumers found, remove additions**
+
+In `flake.nix`, simplify overlays to:
+
+```nix
+overlays = {
+  default = final: prev:
+    import ./pkgs {
+      pkgs = final;
+      inputs = inputs;
+    };
+
+  modifications = final: prev: import ./overlays/mods {inherit prev;};
+};
+```
+
+**Step 3: Verify**
+
+```bash
+nix flake check
+```
+
+**Step 4: Commit**
+
+```bash
+git commit -m "refactor: remove redundant 'additions' overlay (identical to 'default')"
+```
+
+**Note:** If `additions` IS used elsewhere, add a comment explaining the convention and skip this task.
+
+---
+
+## Phase 2: Extract Inline Scripts (Medium Risk)
+
+### Task 4: Extract pi-agent runner script to standalone file
+
+**Objective:** Move the ~200-line inline bash script in `modules/nixos/pi-agent.nix` (the `runner` variable) to a separate file `modules/nixos/pi-agent-runner.sh` that gets imported via `builtins.readFile` + `pkgs.writeShellApplication`.
+
+**Files:**
+- Create: `modules/nixos/pi-agent-runner.sh`
+- Modify: `modules/nixos/pi-agent.nix`
+
+**Step 1: Create the runner script file**
+
+Extract the body of the `runner` script (everything inside the `pkgs.writeShellScriptBin cfg.wrapper.runnerName '' ... ''`) into `modules/nixos/pi-agent-runner.sh`.
+
+The script uses Nix-style variable interpolation (`${...}`). We need to keep Nix template variables as `${...}` and convert runtime bash variables to use `$` prefix. Since the script already uses Nix `escapeShellArg` and `escapeShellArg` calls, the cleanest approach is:
+
+Create `modules/nixos/pi-agent-runner.sh` as a template that `pkgs.substituteAll` or `builtins.readFile` + string replacement can process. However, given the heavy Nix interpolation, the pragmatic approach is to use `pkgs.writeShellApplication` with the script body inline but extracted to a `let` binding:
+
+```nix
+# In pi-agent.nix, replace the inline runner with:
+let
+  runnerScript = builtins.readFile ./pi-agent-runner.sh;
+  # ... or keep as let binding but move the body to a separate derivation
+```
+
+**Important caveat:** The script has ~30 Nix variable interpolations (`${cfg.user}`, `${escapeShellArg ...}`, etc.). Full extraction to a .sh file would require either:
+- (a) `substituteAll` with `--replace` for each variable — unwieldy at 30+ substitutions
+- (b) Converting to env vars passed at runtime — cleaner but changes security posture
+- (c) Keeping the Nix interpolation but extracting to a `let` block in a separate `.nix` file
+
+**Recommended approach: Option (c)** — Create `modules/nixos/pi-agent-runner.nix` as a function that takes `cfg` and returns the script:
+
+```nix
+# modules/nixos/pi-agent-runner.nix
+{cfg, pkgs, lib, ...}:
+with lib; let
+  # ... all the helper variables from pi-agent.nix ...
+in
+  pkgs.writeShellScriptBin cfg.wrapper.runnerName ''
+    # ... the script body ...
+  '';
+```
+
+Then in `pi-agent.nix`:
+```nix
+runner = import ./pi-agent-runner.nix {inherit cfg pkgs lib;};
+```
+
+**Step 2: Similarly extract the wrapper script**
+
+Create `modules/nixos/pi-agent-wrapper.nix` for the `wrapper` variable.
+
+**Step 3: Verify**
+
+```bash
+nix flake check
+# Also test in a nixos-rebuild if possible
+```
+
+**Step 4: Commit**
+
+```bash
+git add modules/nixos/pi-agent-runner.nix modules/nixos/pi-agent-wrapper.nix
+git commit -m "refactor: extract pi-agent runner and wrapper to separate files"
+```
+
+---
+
+## Phase 3: Testing (Higher Value)
+
+### Task 5: Add basic lib function tests
+
+**Objective:** Add `nix eval`-based tests for `lib/agents.nix` parseRule logic and `lib/coding-rules.nix` instruction generation.
+
+**Files:**
+- Create: `tests/lib/agents-test.nix`
+- Create: `tests/lib/coding-rules-test.nix`
+- Modify: `flake.nix` (add checks)
+
+**Step 1: Create test infrastructure**
+
+```nix
+# tests/lib/default.nix
+{
+  agents = import ./agents-test.nix;
+  coding-rules = import ./coding-rules-test.nix;
+}
+```
+
+**Step 2: Write agents.nix parseRule test**
+
+```nix
+# tests/lib/agents-test.nix
+let
+  lib = import <nixpkgs/lib>;
+  agentsLib = (import ../../lib {inherit lib;}).agents;
+
+  # Test parseRule helper
+  test1 = let
+    result = builtins.tryEval (
+      let
+        # We can't directly test parseRule since it's internal.
+        # Instead, test the renderer with minimal input.
+        canonical = {
+          test-agent = {
+            description = "Test agent";
+            mode = "primary";
+            systemPrompt = "You are a test.";
+            permissions = {
+              bash = { intent = "allow"; };
+              edit = { intent = "ask"; rules = ["rm -rf *:deny"]; };
+            };
+          };
+        };
+        pkgs = import <nixpkgs> { system = "x86_64-linux"; };
+        rendered = agentsLib.renderForOpencode {
+          inherit pkgs canonical;
+        };
+      in
+        # Verify the derivation builds
+        builtins.pathExists "${rendered}/test-agent.md"
+    );
+  in assert result.value == true; true;
+
+in {
+  parseRule-basic = test1;
+}
+```
+
+**Step 3: Write coding-rules test**
+
+```nix
+# tests/lib/coding-rules-test.nix
+let
+  lib = import <nixpkgs/lib>;
+  codingRulesLib = (import ../../lib {inherit lib;}).coding-rules;
+
+  rules = codingRulesLib.mkCodingRules {
+    agents = "/tmp/fake-agents";
+    languages = ["python"];
+    concerns = ["naming"];
+    rulesDir = ".coding-rules";
+  };
+
+  # Verify instructions are generated correctly
+  test1 = assert rules.instructions == [
+    ".coding-rules/concerns/naming.md"
+    ".coding-rules/languages/python.md"
+  ]; true;
+
+  # Verify backward-compat alias exists
+  test2 = assert codingRulesLib.mkOpencodeRules == codingRulesLib.mkCodingRules; true;
+
+in {
+  instructions-correct = test1;
+  backward-compat = test2;
+}
+```
+
+**Step 4: Add to flake.nix checks**
+
+In `flake.nix`, extend the `checks` attribute:
+
+```nix
+checks = forAllSystems (system: let
+  pkgs = pkgsFor system;
+  packages = import ./pkgs {inherit pkgs inputs;};
+in
+  builtins.mapAttrs (name: pkg: pkgs.lib.hydraJob pkg) packages
+  // {
+    formatting = pkgs.runCommand "check-formatting" {} ''
+      ${pkgs.alejandra}/bin/alejandra --check ${./.}
+      touch $out
+    '';
+    lib-tests = pkgs.runCommand "lib-tests" {} ''
+      ${pkgs.nix}/bin/nix-instantiate --eval ${./tests/lib/default.nix}
+      touch $out
+    '';
+  });
+```
+
+**Step 5: Verify**
+
+```bash
+nix flake check
+```
+
+**Step 6: Commit**
+
+```bash
+git add tests/
+git commit -m "test: add basic lib function tests for agents and coding-rules"
+```
+
+---
+
+### Task 6: Add NixOS VM test for pi-agent module
+
+**Objective:** Add a basic NixOS VM test that verifies the pi-agent module can be evaluated and the wrapper/runner scripts exist.
+
+**Files:**
+- Create: `tests/nixos/pi-agent-test.nix`
+- Modify: `flake.nix` (add to checks)
+
+**Step 1: Write the VM test**
+
+```nix
+# tests/nixos/pi-agent-test.nix
+{pkgs, ...}: {
+  name = "pi-agent";
+
+  nodes.machine = {config, ...}: {
+    imports = [
+      ${(pkgs.path + "/nixos/modules/module-list.nix")}
+    ];
+
+    # Minimal pi-agent config
+    m3ta.pi-agent = {
+      enable = true;
+      package = pkgs.writeScriptBin "pi-agent" ''
+        #!/bin/sh
+        echo "pi-agent mock"
+      '';
+      createUser = true;
+      hostUsers = {
+        testuser = {
+          projectRoots = ["/tmp/test-project"];
+        };
+      };
+    };
+
+    users.users.testuser = {
+      isNormalUser = true;
+    };
+  };
+
+  testScript = ''
+    machine.start()
+    machine.wait_for_unit("multi-user.target")
+
+    # Verify user was created
+    machine.succeed("id pi-agent")
+
+    # Verify wrapper exists
+    machine.succeed("which pi")
+
+    # Verify state directory
+    machine.succeed("test -d /var/lib/pi-agent")
+    machine.succeed("test -d /var/lib/pi-agent/.pi")
+  '';
+}
+```
+
+**Step 2: Add to flake.nix checks**
+
+```nix
+# In the checks attrset:
+pi-agent-vm-test = pkgs.nixosTest (import ./tests/nixos/pi-agent-test.nix {inherit pkgs;});
+```
+
+**Step 3: Verify**
+
+```bash
+nix build .#checks.x86_64-linux.pi-agent-vm-test
+```
+
+**Step 4: Commit**
+
+```bash
+git add tests/nixos/
+git commit -m "test: add NixOS VM test for pi-agent module"
+```
+
+---
+
+## Phase 4: Documentation (Low Risk, High Value)
+
+### Task 7: Update AGENTS.md to reflect current state
+
+**Objective:** Remove outdated migration sections, update function signatures, and align with current code.
+
+**Files:**
+- Modify: `AGENTS.md`
+
+**Step 1: Update the AGENTS REWORK migration section**
+
+The section starting with `## MIGRATION: Agent System (OpenCode → Canonical TOML)` describes a completed migration. Convert it to a brief "Architecture" section that describes the current state, not the migration path.
+
+**Step 2: Update lib.agents function table**
+
+Verify that the function signatures and descriptions in the AGENTS.md table match the actual functions in `lib/agents.nix`. Specifically:
+- `loadCanonical` takes `{agentsInput}` — confirm docs match
+- `renderForPi` now has `primaryAgent` parameter — confirm documented
+- `shellHookForTool` exists — confirm documented
+
+**Step 3: Update coding-rules documentation**
+
+Replace references to `mkOpencodeRules` with `mkCodingRules` as primary, `mkOpencodeRules` as backward-compat alias. Document the new `rulesDir` parameter.
+
+**Step 4: Update overlay documentation**
+
+Remove or annotate the `additions` overlay depending on Task 3 outcome.
+
+**Step 5: Commit**
+
+```bash
+git commit -m "docs: update AGENTS.md to reflect current codebase state"
+```
+
+---
+
+### Task 8: Add CHANGELOG.md
+
+**Objective:** Create a changelog that captures recent work (from git log) so consumers can track changes.
+
+**Files:**
+- Create: `CHANGELOG.md`
+
+**Step 1: Generate changelog from git history**
+
+```bash
+cd /data/.hermes/repos/nixpkgs-review
+git log --oneline --no-merges master | head -30
+```
+
+**Step 2: Write CHANGELOG.md**
+
+Structure as Keep a Changelog format:
+
+```markdown
+# Changelog
+
+All notable changes to this project will be documented in this file.
+
+The format is based on [Keep a Changelog](https://keepachangelog.com/).
+
+## [Unreleased]
+
+## [0.4.0] - 2026-04-15
+
+### Added
+- Pi agent wrapper with per-host-user policy enforcement (`m3ta.pi-agent` NixOS module)
+- `coding.agents.pi` Home Manager module with settings, MCP, and skills support
+- `coding.agents.claude-code` Home Manager module with MCP integration
+- Automated package updates via Gitea Actions (`nix-update` workflow)
+- `lib.agents.renderForPi` with primaryAgent selection and pi-subagents format
+- `pkgs/td` - Task management CLI for AI coding sessions
+
+### Changed
+- Renamed `lib.opencode-rules` → `lib.coding-rules` (backward-compat alias preserved)
+- Agent system migrated to harness-agnostic canonical format
+- Pi settings sync now merges host and Nix-managed values via deep_merge
+
+### Fixed
+- Pi settings sync race condition on first run
+```
+
+**Step 3: Commit**
+
+```bash
+git commit -m "docs: add CHANGELOG.md"
+```
+
+---
+
+## Phase 5: Minor Cleanups (Low Risk)
+
+### Task 9: Clean up pkgs/default.nix unused `system` binding
+
+**Objective:** The `system = pkgs.stdenv.hostPlatform.system;` binding in `pkgs/default.nix` is only used for the two input-pass-throughs. If those are the only consumers, it's fine, but add a clarifying comment.
+
+**Files:**
+- Modify: `pkgs/default.nix`
+
+**Step 1: Add clarifying comment**
+
+```nix
+{
+  pkgs,
+  inputs,
+  ...
+}: let
+  # Only used for flake input pass-throughs below
+  system = pkgs.stdenv.hostPlatform.system;
+in {
+  ...
+```
+
+**Step 2: Commit**
+
+```bash
+git commit -m "docs: clarify system binding in pkgs/default.nix"
+```
+
+---
+
+### Task 10: Remove commented-out overlay entries in overlays/default.nix
+
+**Objective:** Clean up the large block of commented-out code in `overlays/default.nix` (nodejs_24, paperless-ngx, anytype-heart, hyprpanel, etc.). These belong in git history, not in active code.
+
+**Files:**
+- Modify: `overlays/default.nix`
+
+**Step 1: Remove commented-out blocks**
+
+Remove:
+- The `rose-pine-hyprcursor` addition from `additions` (if it's unused — check with grep)
+- The commented-out `nodejs_24`, `paperless-ngx`, `anytype-heart`, `trezord`, `mesa`, `hyprpanel` blocks from `modifications`
+- The commented-out overlay inputs (`temp-packages`, `stable-packages`, `pinned-packages`, `locked-packages`, `master-packages`) if they reference inputs not in `flake.nix`
+
+Actually, `nixpkgs-stable`, `nixpkgs-9e9486b`, `nixpkgs-9472de4`, `nixpkgs-locked`, `nixpkgs-master` are NOT in the current `flake.nix` inputs. These overlays will fail if referenced. They should either be removed or the inputs should be added.
+
+**Action:**
+- Keep `master-packages` IF `nixpkgs-master` is in flake.nix inputs (it IS — good)
+- Remove `temp-packages`, `pinned-packages`, `locked-packages` (inputs don't exist)
+- Keep `stable-packages` IF `nixpkgs-stable` exists in inputs (check — it does NOT currently exist)
+- Keep `additions` with `rose-pine-hyprcursor` IF `rose-pine-hyprcursor` input exists (check)
+
+**Step 2: Verify**
+
+```bash
+nix flake check
+```
+
+**Step 3: Commit**
+
+```bash
+git commit -m "chore: remove dead overlay entries for non-existent flake inputs"
+```
+
+---
+
+## Execution Order & Priority
+
+| Task | Risk | Effort | Impact | Dependencies |
+|------|------|--------|--------|-------------|
+| T1: Remove opencode-rules.nix | Low | 5min | Clean | None |
+| T2: Tool-agnostic naming | Low | 15min | Consistency | None |
+| T3: Remove redundant overlay | Low | 10min | Clean | Check consumers |
+| T9: Clarify system binding | Low | 2min | Docs | None |
+| T10: Remove dead overlays | Low | 10min | Clean | None |
+| T7: Update AGENTS.md | Low | 20min | Docs | After T1, T2 |
+| T8: Add CHANGELOG.md | Low | 15min | Docs | None |
+| T4: Extract pi-agent scripts | Medium | 45min | Maintainability | None |
+| T5: Lib function tests | Medium | 30min | Quality | None |
+| T6: NixOS VM test | Medium | 45min | Quality | None |
+
+**Recommended order:** T1 → T9 → T10 → T3 → T2 → T7 → T8 → T5 → T4 → T6
+
+**Branching strategy:** Create a feature branch `chore/cleanup-review` from master, implement all tasks, open PR for review before merging.

flake.nix

@@ -56,13 +56,6 @@
           inputs = inputs;
         };
 
-      # Individual overlays for more granular control
-      additions = final: prev:
-        import ./pkgs {
-          pkgs = final;
-          inputs = inputs;
-        };
-
       modifications = final: prev: import ./overlays/mods {inherit prev;};
     };
 
@@ -72,6 +65,7 @@
       # Individual modules for selective imports
       ports = ./modules/nixos/ports.nix;
       mem0 = ./modules/nixos/mem0.nix;
+      pi-agent = ./modules/nixos/pi-agent.nix;
     };
 
     # Home Manager modules - for user-level configuration

lib/coding-rules.nix

@@ -26,7 +26,7 @@
 #
 # The shellHook creates:
 #   - A `.opencode-rules/` symlink pointing to the AGENTS repository rules directory
-#   - An `opencode.json` file with a $schema reference and instructions list
+#   - A `coding-rules.json` file with a $schema reference and instructions list
 #
 # The instructions list contains paths relative to the project root, all prefixed
 # with `.opencode-rules/`, making them portable across different project locations.
@@ -46,7 +46,7 @@
   #
   # Returns:
   #   An attribute set containing:
-  #     - shellHook: Bash code to create symlink and opencode.json
+  #     - shellHook: Bash code to create symlink and coding-rules.json
   #     - instructions: List of rule file paths (relative to project root)
   #
   # Example:
@@ -82,9 +82,8 @@
     ],
     frameworks ? [],
     extraInstructions ? [],
+    rulesDir ? ".opencode-rules",
   }: let
-    rulesDir = ".opencode-rules";
-
     # Build instructions list by mapping concerns, languages, frameworks to their file paths
     # All paths are relative to project root via the rulesDir symlink
     instructions =
@@ -93,8 +92,8 @@
       ++ (map (f: "${rulesDir}/frameworks/${f}.md") frameworks)
       ++ extraInstructions;
 
-    # Generate JSON configuration for Opencode
+    # Generate JSON configuration for coding rules
-    opencodeConfig = {
+    rulesConfig = {
       "$schema" = "https://opencode.ai/config.json";
       inherit instructions;
     };
@@ -102,15 +101,15 @@
     inherit instructions;
 
     # Shell hook to set up rules in the project
-    # Creates a symlink to the AGENTS rules directory and generates opencode.json
+    # Creates a symlink to the AGENTS rules directory and generates coding-rules.json
     shellHook = ''
       # Create/update symlink to AGENTS rules directory
       ln -sfn ${agents}/rules ${rulesDir}
 
-      # Generate opencode.json configuration file
+      # Generate coding-rules.json configuration file
-      cat > opencode.json <<'OPENCODE_EOF'
+      cat > coding-rules.json <<'RULES_EOF'
-      ${builtins.toJSON opencodeConfig}
+      ${builtins.toJSON rulesConfig}
-      OPENCODE_EOF
+      RULES_EOF
     '';
   };
 

lib/opencode-rules.nix

@@ -1,116 +0,0 @@
-# Opencode rules management utilities
-#
-# This module provides functions to configure Opencode agent rules across
-# multiple projects. Rules are defined in the AGENTS repository and can be
-# selectively included based on language, framework, and concerns.
-#
-# Usage in your configuration:
-#
-#   # In your flake or configuration:
-#   let
-#     m3taLib = inputs.m3ta-nixpkgs.lib.${system};
-#
-#     rules = m3taLib.opencode-rules.mkOpencodeRules {
-#       agents = inputs.agents;
-#       languages = [ "python" "typescript" ];
-#       concerns = [ "coding-style" "naming" "documentation" ];
-#       frameworks = [ "react" "fastapi" ];
-#     };
-#   in {
-#     # Use in your devShell:
-#     devShells.default = pkgs.mkShell {
-#       shellHook = rules.shellHook;
-#       inherit (rules) instructions;
-#     };
-#   }
-#
-# The shellHook creates:
-#   - A `.opencode-rules/` symlink pointing to the AGENTS repository rules directory
-#   - An `opencode.json` file with a $schema reference and instructions list
-#
-# The instructions list contains paths relative to the project root, all prefixed
-# with `.opencode-rules/`, making them portable across different project locations.
-{lib}: {
-  # Create Opencode rules configuration from AGENTS repository
-  #
-  # Args:
-  #   agents: Path to the AGENTS repository (non-flake input)
-  #   languages: Optional list of language-specific rules to include
-  #              (e.g., [ "python" "typescript" "rust" ])
-  #   concerns: Optional list of concern rules to include
-  #             Default: [ "coding-style" "naming" "documentation" "testing" "git-workflow" "project-structure" ]
-  #   frameworks: Optional list of framework-specific rules to include
-  #               (e.g., [ "react" "fastapi" "django" ])
-  #   extraInstructions: Optional list of additional instruction paths
-  #                      (for custom rules outside standard locations)
-  #
-  # Returns:
-  #   An attribute set containing:
-  #     - shellHook: Bash code to create symlink and opencode.json
-  #     - instructions: List of rule file paths (relative to project root)
-  #
-  # Example:
-  #   mkOpencodeRules {
-  #     agents = inputs.agents;
-  #     languages = [ "python" ];
-  #     frameworks = [ "fastapi" ];
-  #   }
-  #   # Returns:
-  #   # {
-  #   #   shellHook = "...";
-  #   #   instructions = [
-  #   #     ".opencode-rules/concerns/coding-style.md"
-  #   #     ".opencode-rules/concerns/naming.md"
-  #   #     ".opencode-rules/concerns/documentation.md"
-  #   #     ".opencode-rules/concerns/testing.md"
-  #   #     ".opencode-rules/concerns/git-workflow.md"
-  #   #     ".opencode-rules/concerns/project-structure.md"
-  #   #     ".opencode-rules/languages/python.md"
-  #   #     ".opencode-rules/frameworks/fastapi.md"
-  #   #   ];
-  #   # }
-  mkOpencodeRules = {
-    agents,
-    languages ? [],
-    concerns ? [
-      "coding-style"
-      "naming"
-      "documentation"
-      "testing"
-      "git-workflow"
-      "project-structure"
-    ],
-    frameworks ? [],
-    extraInstructions ? [],
-  }: let
-    rulesDir = ".opencode-rules";
-
-    # Build instructions list by mapping concerns, languages, frameworks to their file paths
-    # All paths are relative to project root via the rulesDir symlink
-    instructions =
-      (map (c: "${rulesDir}/concerns/${c}.md") concerns)
-      ++ (map (l: "${rulesDir}/languages/${l}.md") languages)
-      ++ (map (f: "${rulesDir}/frameworks/${f}.md") frameworks)
-      ++ extraInstructions;
-
-    # Generate JSON configuration for Opencode
-    opencodeConfig = {
-      "$schema" = "https://opencode.ai/config.json";
-      inherit instructions;
-    };
-  in {
-    inherit instructions;
-
-    # Shell hook to set up rules in the project
-    # Creates a symlink to the AGENTS rules directory and generates opencode.json
-    shellHook = ''
-      # Create/update symlink to AGENTS rules directory
-      ln -sfn ${agents}/rules ${rulesDir}
-
-      # Generate opencode.json configuration file
-      cat > opencode.json <<'OPENCODE_EOF'
-      ${builtins.toJSON opencodeConfig}
-      OPENCODE_EOF
-    '';
-  };
-}

modules/home-manager/AGENTS.md

@@ -119,23 +119,26 @@ coding.agents.claude-code = {
   enable = true;
   agentsInput = inputs.agents;
   modelOverrides = {};
+  externalSkills = [{ src = inputs.skills-anthropic; }];
 };
 ```
 
-**Options:** `enable`, `agentsInput`, `modelOverrides`
+**Options:** `enable`, `agentsInput`, `modelOverrides`, `externalSkills`
 
 ### Pi (`coding.agents.pi`)
 
-Renders `AGENTS.md` + `SYSTEM.md` to `~/.pi/agent/`:
+Renders `AGENTS.md` + `SYSTEM.md` to `~/.pi/agent/` by default:
 
 ```nix
 coding.agents.pi = {
   enable = true;
   agentsInput = inputs.agents;
+  path = ".pi/agent"; # default, relative to $HOME
+  externalSkills = [{ src = inputs.skills-anthropic; }];
 };
 ```
 
-**Options:** `enable`, `agentsInput`
+**Options:** `enable`, `path`, `agentsInput`, `modelOverrides`, `externalSkills`, `primaryAgent`, `mcpServers`, `settings`
 
 ### Project-level usage
 

modules/home-manager/coding/agents/claude-code.nix

@@ -36,9 +36,50 @@ in {
       '';
     };
 
+    externalSkills = mkOption {
+      type = types.listOf (types.submodule {
+        options = {
+          src = mkOption {
+            type = types.anything;
+            description = "Flake input pointing to a skills repository root.";
+          };
+          skillsDir = mkOption {
+            type = types.str;
+            default = "skills";
+            description = ''
+              Subdirectory inside src that contains skill folders.
+            '';
+          };
+          selectSkills = mkOption {
+            type = types.nullOr (types.listOf types.str);
+            default = null;
+            description = ''
+              List of skill names to cherry-pick from this source.
+              null means include every skill found in skillsDir.
+            '';
+          };
+        };
+      });
+      default = [];
+      description = ''
+        External skill sources passed to mkOpencodeSkills.
+        Each entry maps directly to an element of the externalSkills
+        list accepted by the AGENTS flake's lib.mkOpencodeSkills.
+      '';
+      example = literalExpression ''
+        [
+          { src = inputs.skills-anthropic; selectSkills = [ "claude-api" ]; }
+          { src = inputs.skills-vercel; }
+        ]
+      '';
+    };
+
     mcpServers = mkOption {
       type = types.attrsOf types.anything;
-      default = if mcpCfg != null then mcpCfg.servers else {};
+      default =
+        if mcpCfg != null
+        then mcpCfg.servers
+        else {};
       defaultText = literalExpression "config.programs.mcp.servers";
       description = ''
         MCP server configurations for Claude Code.
@@ -82,6 +123,21 @@ in {
       source = "${rendered}/.claude/agents";
     };
 
+    # Skills (merged from personal AGENTS repo + optional external skills)
+    home.file.".claude/skills" = mkIf (cfg.agentsInput != null) {
+      source = cfg.agentsInput.lib.mkOpencodeSkills {
+        inherit pkgs;
+        customSkills = "${cfg.agentsInput}/skills";
+        externalSkills =
+          map (
+            entry:
+              {inherit (entry) src skillsDir;}
+              // optionalAttrs (entry.selectSkills != null) {inherit (entry) selectSkills;}
+          )
+          cfg.externalSkills;
+      };
+    };
+
     # Rendered settings.json with permissions + MCP servers
     home.file.".claude/settings.json" = mkIf (settingsJson != null) {
       source = "${settingsJson}";

modules/home-manager/coding/agents/pi.nix

@@ -11,13 +11,28 @@ in {
   options.coding.agents.pi = {
     enable = mkEnableOption "Pi agent management via canonical agent.toml definitions";
 
+    path = mkOption {
+      type = types.str;
+      default = ".pi/agent";
+      description = ''
+        Relative path (inside the Home Manager user's home) where Pi agent
+        config should be materialized.
+
+        Defaults to `.pi/agent`, i.e. `~/.pi/agent`.
+      '';
+      example = ".config/pi/agent";
+    };
+
     mcpServers = mkOption {
       type = types.attrsOf types.anything;
-      default = if mcpCfg != null then mcpCfg.servers else {};
+      default =
+        if mcpCfg != null
+        then mcpCfg.servers
+        else {};
       defaultText = literalExpression "config.programs.mcp.servers";
       description = ''
         MCP server configurations for Pi (pi-mcp-adapter).
-        Written to ~/.pi/agent/mcp.json.
+        Written to `${cfg.path}/mcp.json`.
         Automatically inherits from config.programs.mcp.servers.
       '';
     };
@@ -42,6 +57,44 @@ in {
       '';
     };
 
+    externalSkills = mkOption {
+      type = types.listOf (types.submodule {
+        options = {
+          src = mkOption {
+            type = types.anything;
+            description = "Flake input pointing to a skills repository root.";
+          };
+          skillsDir = mkOption {
+            type = types.str;
+            default = "skills";
+            description = ''
+              Subdirectory inside src that contains skill folders.
+            '';
+          };
+          selectSkills = mkOption {
+            type = types.nullOr (types.listOf types.str);
+            default = null;
+            description = ''
+              List of skill names to cherry-pick from this source.
+              null means include every skill found in skillsDir.
+            '';
+          };
+        };
+      });
+      default = [];
+      description = ''
+        External skill sources passed to mkOpencodeSkills.
+        Each entry maps directly to an element of the externalSkills
+        list accepted by the AGENTS flake's lib.mkOpencodeSkills.
+      '';
+      example = literalExpression ''
+        [
+          { src = inputs.skills-anthropic; selectSkills = [ "claude-api" ]; }
+          { src = inputs.skills-vercel; }
+        ]
+      '';
+    };
+
     primaryAgent = mkOption {
       type = types.nullOr types.str;
       default = null;
@@ -60,7 +113,7 @@ in {
             default = [];
             description = ''
               Pi packages to install (npm:, git:, or local paths).
-              These are written to ~/.pi/agent/settings.json.
+              These are written to `${cfg.path}/settings.json`.
             '';
           };
 
@@ -148,7 +201,7 @@ in {
       };
       default = {};
       description = ''
-        Pi settings written to ~/.pi/agent/settings.json.
+        Pi settings written to `${cfg.path}/settings.json`.
         Only non-null values are included in the generated JSON.
         See pi docs/settings.md for all options.
       '';
@@ -156,6 +209,8 @@ in {
   };
 
   config = mkIf cfg.enable (let
+    basePath = lib.removeSuffix "/" cfg.path;
+
     # Build settings.json by filtering out null values recursively
     filterNulls = attrs:
       lib.filterAttrs (_: v: v != null) (
@@ -164,8 +219,11 @@ in {
           then let
             filtered = filterNulls v;
           in
-            if filtered == {} then null else filtered
+            if filtered == {}
-          else v) attrs
+            then null
+            else filtered
+          else v)
+        attrs
       );
 
     piSettings = filterNulls cfg.settings;
@@ -185,38 +243,37 @@ in {
     # Dynamic home.file entries for agent .md files
     agentFiles =
       if cfg.agentsInput != null
-      then
+      then let
-        let
+        agentNames = builtins.attrNames cfg.agentsInput.lib.loadAgents;
-          agentNames = builtins.attrNames cfg.agentsInput.lib.loadAgents;
+      in
-        in
+        builtins.listToAttrs (
-          builtins.listToAttrs (
+          map (name: {
-            map (name: {
+            name = "${basePath}/agents/${name}.md";
-              name = ".pi/agent/agents/${name}.md";
+            value = {source = "${rendered}/agents/${name}.md";};
-              value = {source = "${rendered}/agents/${name}.md";};
+          })
-            })
+          agentNames
-            agentNames
+        )
-          )
       else {};
   in {
     home.file = mkMerge [
-      # ── MCP servers from programs.mcp → ~/.pi/agent/mcp.json ───────
+      # ── MCP servers from programs.mcp → ${cfg.path}/mcp.json ───────
       (mkIf (cfg.mcpServers != {}) {
-        ".pi/agent/mcp.json".text = builtins.toJSON {mcpServers = cfg.mcpServers;};
+        "${basePath}/mcp.json".text = builtins.toJSON {mcpServers = cfg.mcpServers;};
       })
 
-      # ── ~/.pi/agent/settings.json ──────────────────────────────────
+      # ── ${cfg.path}/settings.json ──────────────────────────────────
       {
-        ".pi/agent/settings.json".text = builtins.toJSON piSettings;
+        "${basePath}/settings.json".text = builtins.toJSON piSettings;
       }
 
       # ── AGENTS.md — agent descriptions and specialist listing ──────
       (mkIf (cfg.agentsInput != null) {
-        ".pi/agent/AGENTS.md".source = "${rendered}/AGENTS.md";
+        "${basePath}/AGENTS.md".source = "${rendered}/AGENTS.md";
       })
 
       # ── SYSTEM.md — primary agent's system prompt ──────────────────
       (mkIf (cfg.agentsInput != null) {
-        ".pi/agent/SYSTEM.md".source = "${rendered}/SYSTEM.md";
+        "${basePath}/SYSTEM.md".source = "${rendered}/SYSTEM.md";
       })
 
       # ── Agents — pi-subagents .md files ────────────────────────────
@@ -224,9 +281,16 @@ in {
 
       # ── Skills symlinked from AGENTS repo ──────────────────────────
       (mkIf (cfg.agentsInput != null) {
-        ".pi/agent/skills".source = cfg.agentsInput.lib.mkOpencodeSkills {
+        "${basePath}/skills".source = cfg.agentsInput.lib.mkOpencodeSkills {
           inherit pkgs;
           customSkills = "${cfg.agentsInput}/skills";
+          externalSkills =
+            map (
+              entry:
+                {inherit (entry) src skillsDir;}
+                // optionalAttrs (entry.selectSkills != null) {inherit (entry) selectSkills;}
+            )
+            cfg.externalSkills;
         };
       })
     ];

modules/nixos/default.nix

@@ -13,6 +13,7 @@
   imports = [
     ./mem0.nix
     ./ports.nix
+    ./pi-agent.nix
     # Example: ./my-service.nix
     # Add more module files here as you create them
   ];

modules/nixos/pi-agent-runner.nix

@@ -0,0 +1,401 @@
+{
+  cfg,
+  pkgs,
+  lib,
+  ...
+}:
+with lib; let
+  managedSettingsFile = pkgs.writeText "pi-agent-managed-settings.json" (builtins.toJSON cfg.settings);
+
+  managedEnvFile =
+    pkgs.writeText "pi-agent-managed.env"
+    (concatStringsSep "\n" (mapAttrsToList (k: v: "${k}=${v}") cfg.environment));
+
+  runtimePath = concatStringsSep ":" (
+    [
+      "${cfg.package}/bin"
+      "${pkgs.nodejs}/bin"
+      "${pkgs.git}/bin"
+      "${pkgs.coreutils}/bin"
+      "${pkgs.findutils}/bin"
+      "${pkgs.gnugrep}/bin"
+      "${pkgs.gnused}/bin"
+      "${pkgs.util-linux}/bin"
+      "/run/current-system/sw/bin"
+    ]
+    ++ map (p: "${p}/bin") cfg.extraPackages
+  );
+
+  userPolicyCase = concatStringsSep "\n" (
+    mapAttrsToList (
+      user: userCfg: ''
+        ${escapeShellArg user})
+          USER_CONFIG_PATH=${escapeShellArg (
+          if userCfg.configPath != null
+          then userCfg.configPath
+          else cfg.wrapper.hostConfigPath
+        )}
+          USER_ROOTS=(${concatStringsSep " " (map escapeShellArg userCfg.projectRoots)})
+          ;;
+      ''
+    )
+    cfg.hostUsers
+  );
+in
+  pkgs.writeShellScriptBin cfg.wrapper.runnerName ''
+        set -euo pipefail
+
+        if [ "$(id -u)" -ne 0 ]; then
+          echo "${cfg.wrapper.runnerName} must run as root" >&2
+          exit 1
+        fi
+
+        if [ "$#" -lt 2 ]; then
+          echo "Usage: ${cfg.wrapper.runnerName} <invoking-user> <cwd> [pi-args...]" >&2
+          exit 2
+        fi
+
+        invoking_user="$1"
+        shift
+        cwd="$1"
+        shift
+
+        # Parse forwarded environment variables from wrapper (KEY=VALUE)
+        while [ "$#" -gt 0 ]; do
+          case "$1" in
+            TERM=*|LANG=*|LC_ALL=*|LC_CTYPE=*|COLORTERM=*|TERM_PROGRAM=*)
+              export "$1"
+              shift
+              ;;
+            *)
+              break
+              ;;
+          esac
+        done
+
+        resolve_user_policy() {
+          local user="$1"
+          USER_CONFIG_PATH=""
+          USER_ROOTS=()
+          case "$user" in
+            ${userPolicyCase}
+            *)
+              return 1
+              ;;
+          esac
+          return 0
+        }
+
+        if ! resolve_user_policy "$invoking_user"; then
+          echo "User '$invoking_user' is not allowed to use ${cfg.wrapper.commandName}" >&2
+          exit 1
+        fi
+
+        user_home="$(eval echo "~$invoking_user")"
+        if [ -z "$user_home" ] || [ "$user_home" = "~$invoking_user" ]; then
+          echo "Unable to determine home directory for user '$invoking_user'" >&2
+          exit 1
+        fi
+
+        expand_home_path() {
+          local input="$1"
+          if [ "$input" = "~" ]; then
+            printf '%s\n' "$user_home"
+          elif ${pkgs.gnugrep}/bin/grep -q '^~/' <<<"$input"; then
+            printf '%s\n' "$user_home/''${input:2}"
+          elif ${pkgs.gnugrep}/bin/grep -q '^/' <<<"$input"; then
+            printf '%s\n' "$input"
+          else
+            # Bare relative path → resolve from user's home
+            printf '%s\n' "$user_home/$input"
+          fi
+        }
+
+        cwd_real="$(${pkgs.coreutils}/bin/realpath -m "$cwd")"
+
+        resolved_roots=()
+        skipped_roots=()
+        is_allowed_cwd=0
+        for configured_root in "''${USER_ROOTS[@]}"; do
+          expanded_root="$(expand_home_path "$configured_root")"
+          resolved_root="$(${pkgs.coreutils}/bin/realpath -m "$expanded_root")"
+          if [ ! -d "$resolved_root" ]; then
+            skipped_roots+=("$resolved_root")
+            continue
+          fi
+          resolved_roots+=("$resolved_root")
+          case "$cwd_real/" in
+            "$resolved_root"/*)
+              is_allowed_cwd=1
+              ;;
+          esac
+        done
+
+        if [ "''${#resolved_roots[@]}" -eq 0 ]; then
+          echo "Denied: no valid existing project roots are configured for user '$invoking_user'." >&2
+          if [ "''${#skipped_roots[@]}" -gt 0 ]; then
+            echo "Configured but missing roots:" >&2
+            for root in "''${skipped_roots[@]}"; do
+              echo "  - $root" >&2
+            done
+          fi
+          exit 1
+        fi
+
+        if [ "$is_allowed_cwd" -ne 1 ]; then
+          echo "Denied: '$cwd_real' is outside allowed project roots for user '$invoking_user'." >&2
+          echo "Allowed roots:" >&2
+          for root in "''${resolved_roots[@]}"; do
+            echo "  - $root" >&2
+          done
+          exit 1
+        fi
+
+        ${pkgs.coreutils}/bin/install -d -m 0750 -o ${escapeShellArg cfg.user} -g ${escapeShellArg cfg.group} \
+          ${escapeShellArg cfg.stateDir} \
+          ${escapeShellArg "${cfg.stateDir}/.pi"} \
+          ${escapeShellArg "${cfg.stateDir}/.pi/agent"} \
+          ${escapeShellArg "${cfg.stateDir}/.pi/agent/sessions"} \
+          ${escapeShellArg "${cfg.stateDir}/.project-mounts"} \
+          ${escapeShellArg "${cfg.stateDir}/projects"} \
+          ${escapeShellArg "${cfg.stateDir}/.npm"} \
+          ${escapeShellArg "${cfg.stateDir}/.npm-global"} \
+          ${escapeShellArg "${cfg.stateDir}/.npm-global/bin"} \
+          ${escapeShellArg "${cfg.stateDir}/.npm-global/lib"}
+
+        config_source="$USER_CONFIG_PATH"
+        if ${pkgs.gnugrep}/bin/grep -q '^/' <<<"$config_source"; then
+          source_dir="$config_source"
+        else
+          source_dir="$(expand_home_path "$config_source")"
+        fi
+
+
+        if [ "${
+      if cfg.wrapper.syncConfigFromHost
+      then "1"
+      else "0"
+    }" = "1" ] && [ -d "$source_dir" ]; then
+          ${pkgs.rsync}/bin/rsync -a --delete \
+            --exclude='auth.json' \
+            --exclude='mcp-oauth' \
+            --exclude='sessions' \
+            --exclude='bin' \
+            --exclude='mcp-cache.json' \
+            "$source_dir/" ${escapeShellArg "${cfg.stateDir}/.pi/agent/"}
+          ${pkgs.coreutils}/bin/chown -R ${escapeShellArg "${cfg.user}:${cfg.group}"} ${escapeShellArg "${cfg.stateDir}/.pi/agent"}
+        fi
+
+        # Merge host settings.json (if any) with Nix-managed settings.
+        # Precedence: host settings first, Nix-managed keys override recursively.
+        settings_target=${escapeShellArg "${cfg.stateDir}/.pi/agent/settings.json"}
+        ${pkgs.python3}/bin/python3 - "$settings_target" ${escapeShellArg managedSettingsFile} <<'PY_PI_SETTINGS_MERGE'
+    import json
+    import os
+    import sys
+
+
+    def load_obj(path):
+        if not os.path.exists(path):
+            return {}
+        try:
+            with open(path, "r", encoding="utf-8") as f:
+                data = json.load(f)
+                return data if isinstance(data, dict) else {}
+        except Exception:
+            return {}
+
+
+    def deep_merge(base, override):
+        if isinstance(base, dict) and isinstance(override, dict):
+            out = dict(base)
+            for key, value in override.items():
+                out[key] = deep_merge(out.get(key), value)
+            return out
+        return override
+
+
+    def main():
+        target = sys.argv[1]
+        managed = sys.argv[2]
+        base_obj = load_obj(target)
+        managed_obj = load_obj(managed)
+        merged = deep_merge(base_obj, managed_obj)
+
+        os.makedirs(os.path.dirname(target), exist_ok=True)
+        tmp = f"{target}.tmp"
+        with open(tmp, "w", encoding="utf-8") as f:
+            json.dump(merged, f, indent=2, sort_keys=True)
+            f.write("\n")
+        os.replace(tmp, target)
+
+
+    if __name__ == "__main__":
+        main()
+    PY_PI_SETTINGS_MERGE
+        ${pkgs.coreutils}/bin/chown ${escapeShellArg "${cfg.user}:${cfg.group}"} "$settings_target"
+        ${pkgs.coreutils}/bin/chmod 0640 "$settings_target"
+
+        # Merge environment into isolated .env with precedence:
+        # 1) synced host env (source_dir/.env)
+        # 2) Nix-managed environment attrset
+        # 3) Nix-managed environmentFiles (appended in declaration order)
+        env_target=${escapeShellArg "${cfg.stateDir}/.pi/.env"}
+        ${pkgs.coreutils}/bin/install -o ${escapeShellArg cfg.user} -g ${escapeShellArg cfg.group} -m 0640 /dev/null "$env_target"
+
+        if [ -f "$source_dir/.env" ]; then
+          ${pkgs.coreutils}/bin/cat "$source_dir/.env" >> "$env_target"
+          printf '\n' >> "$env_target"
+        fi
+
+        if [ -f ${escapeShellArg managedEnvFile} ]; then
+          ${pkgs.coreutils}/bin/cat ${escapeShellArg managedEnvFile} >> "$env_target"
+          printf '\n' >> "$env_target"
+        fi
+
+        ${concatStringsSep "\n" (map (f: ''
+        if [ -f ${escapeShellArg f} ]; then
+          ${pkgs.coreutils}/bin/cat ${escapeShellArg f} >> "$env_target"
+          printf '\n' >> "$env_target"
+        fi
+      '')
+      cfg.environmentFiles)}
+
+        ${pkgs.coreutils}/bin/chown ${escapeShellArg "${cfg.user}:${cfg.group}"} "$env_target"
+        ${pkgs.coreutils}/bin/chmod 0640 "$env_target"
+
+        npm_prefix=${escapeShellArg "${cfg.stateDir}/.npm-global"}
+        runtime_path=${escapeShellArg runtimePath}
+
+        project_mount_dir=${escapeShellArg "${cfg.stateDir}/.project-mounts"}
+        project_links_dir=${escapeShellArg "${cfg.stateDir}/projects"}
+        project_bind_pairs=()
+
+        matched_root=""
+        matched_mount=""
+        project_index=0
+
+        for root in "''${resolved_roots[@]}"; do
+          if [ ! -d "$root" ]; then
+            continue
+          fi
+
+          root_slug="$(printf '%s' "$root" | ${pkgs.gnused}/bin/sed 's#^/##; s#/#-#g; s#-\{2,\}#-#g; s#-$##; s#^$#root#')"
+          root_slug="''${project_index}-''${root_slug}"
+          project_index=$((project_index + 1))
+
+          mount_point="''${project_mount_dir}/''${root_slug}"
+          link_path="''${project_links_dir}/''${root_slug}"
+
+          ${pkgs.coreutils}/bin/install -d -m 0750 -o ${escapeShellArg cfg.user} -g ${escapeShellArg cfg.group} "$mount_point"
+          ${pkgs.coreutils}/bin/ln -sfn "$mount_point" "$link_path"
+
+          project_bind_pairs+=("$root:$mount_point")
+
+          case "$cwd_real/" in
+            "$root"/*)
+              if [ -z "$matched_root" ] || [ "''${#root}" -gt "''${#matched_root}" ]; then
+                matched_root="$root"
+                matched_mount="$mount_point"
+              fi
+              ;;
+          esac
+        done
+
+        if [ -z "$matched_root" ]; then
+          echo "Failed to map cwd '$cwd_real' to an allowed root." >&2
+          exit 1
+        fi
+
+        if [ "$cwd_real" = "$matched_root" ]; then
+          mapped_cwd="$matched_mount"
+        else
+          rel_path="''${cwd_real#"$matched_root/"}"
+          mapped_cwd="$matched_mount/$rel_path"
+        fi
+
+        pi_bin=${escapeShellArg "${cfg.package}/bin/${cfg.binaryName}"}
+
+        if [ ! -x "$pi_bin" ]; then
+          for candidate in pi pi-agent; do
+            alt=${escapeShellArg "${cfg.package}/bin"}/$candidate
+            if [ -x "$alt" ]; then
+              pi_bin="$alt"
+              break
+            fi
+          done
+        fi
+
+        if [ ! -x "$pi_bin" ]; then
+          echo "Pi binary not found or not executable: $pi_bin" >&2
+          echo "Available executables in ${cfg.package}/bin:" >&2
+          ${pkgs.coreutils}/bin/ls -1 ${escapeShellArg "${cfg.package}/bin"} >&2 || true
+          exit 127
+        fi
+
+        cmd=(
+          ${pkgs.systemd}/bin/systemd-run
+          --collect
+          --wait
+          --pty
+          --service-type=exec
+          -p User=${cfg.user}
+          -p Group=${cfg.group}
+          -p WorkingDirectory="$mapped_cwd"
+          -p NoNewPrivileges=yes
+          -p PrivateTmp=yes
+          -p ProtectSystem=strict
+          -p ProtectHome=false
+          -p ProtectControlGroups=yes
+          -p ProtectKernelTunables=yes
+          -p ProtectKernelModules=yes
+          -p RestrictSUIDSGID=yes
+          -p LockPersonality=yes
+          -p RestrictRealtime=yes
+          -p RestrictNamespaces=yes
+          -p MemoryDenyWriteExecute=no
+          -p UMask=0007
+          -p ReadWritePaths=${cfg.stateDir}
+          -p EnvironmentFile=${cfg.stateDir}/.pi/.env
+          -E HOME=${cfg.stateDir}
+          -E PI_HOME=${cfg.stateDir}/.pi
+          -E MESSAGING_CWD="$mapped_cwd"
+          -E PATH="$runtime_path"
+          -E NPM_CONFIG_CACHE=${cfg.stateDir}/.npm
+          -E NPM_CONFIG_PREFIX="$npm_prefix"
+          -E PI_AGENT_INVOKING_USER="$invoking_user"
+        )
+
+        # Propagate terminal and locale settings for correct PTY/UTF-8 handling
+        for env_var in TERM LANG LC_ALL LC_CTYPE COLORTERM TERM_PROGRAM; do
+          if [ -n "''${!env_var:-}" ]; then
+            cmd+=( -E "$env_var=''${!env_var}" )
+          fi
+        done
+
+        ${optionalString (cfg.projectGroup != null) ''
+      cmd+=( -p SupplementaryGroups=${cfg.projectGroup} )
+    ''}
+
+        # Only mark existing top-level paths inaccessible; systemd fails namespace
+        # setup if InaccessiblePaths points to a non-existent path on this host.
+        for p in /home /root /mnt /media /srv; do
+          if [ -e "$p" ]; then
+            cmd+=( -p "InaccessiblePaths=$p" )
+          fi
+        done
+
+        for pair in "''${project_bind_pairs[@]}"; do
+          src="''${pair%%:*}"
+          dst="''${pair#*:}"
+          cmd+=( -p "BindPaths=$src:$dst" )
+        done
+
+        ${concatStringsSep "\n" (mapAttrsToList (name: value: ''cmd+=( -E ${escapeShellArg "${name}=${value}"} )'') cfg.wrapper.extraEnvironment)}
+
+        cmd+=( "$pi_bin" )
+        ${concatStringsSep "\n" (map (arg: ''cmd+=( ${escapeShellArg arg} )'') cfg.wrapper.extraRunArgs)}
+        cmd+=( "$@" )
+
+        exec "''${cmd[@]}"
+  ''

modules/nixos/pi-agent-wrapper.nix

@@ -0,0 +1,102 @@
+{
+  cfg,
+  pkgs,
+  lib,
+  runner,
+  ...
+}:
+with lib;
+  pkgs.writeShellScriptBin cfg.wrapper.commandName ''
+    set -euo pipefail
+
+    user_name="$(id -un)"
+    user_home="$(eval echo "~$user_name")"
+    if [ -z "$user_home" ] || [ "$user_home" = "~$user_name" ]; then
+      user_home="$HOME"
+    fi
+
+    resolve_user_policy() {
+      local user="$1"
+      USER_ROOTS=()
+      case "$user" in
+        ${concatStringsSep "\n" (
+      mapAttrsToList (
+        user: userCfg: ''
+          ${escapeShellArg user})
+            USER_ROOTS=(${concatStringsSep " " (map escapeShellArg userCfg.projectRoots)})
+            ;;
+        ''
+      )
+      cfg.hostUsers
+    )}
+        *)
+          return 1
+          ;;
+      esac
+      return 0
+    }
+
+    if ! resolve_user_policy "$user_name"; then
+      echo "User '$user_name' is not allowed to use ${cfg.wrapper.commandName}" >&2
+      exit 1
+    fi
+
+    expand_home_path() {
+      local input="$1"
+      if [ "$input" = "~" ]; then
+        printf '%s\n' "$user_home"
+      elif ${pkgs.gnugrep}/bin/grep -q '^~/' <<<"$input"; then
+        printf '%s\n' "$user_home/''${input:2}"
+      elif ${pkgs.gnugrep}/bin/grep -q '^/' <<<"$input"; then
+        printf '%s\n' "$input"
+      else
+        printf '%s\n' "$user_home/$input"
+      fi
+    }
+
+    cwd_real="$(${pkgs.coreutils}/bin/realpath -m "$PWD")"
+
+    is_allowed_cwd=0
+    resolved_roots=()
+    skipped_roots=()
+    for configured_root in "''${USER_ROOTS[@]}"; do
+      expanded_root="$(expand_home_path "$configured_root")"
+      resolved_root="$(${pkgs.coreutils}/bin/realpath -m "$expanded_root")"
+      if [ ! -d "$resolved_root" ]; then
+        skipped_roots+=("$resolved_root")
+        continue
+      fi
+      resolved_roots+=("$resolved_root")
+      case "$cwd_real/" in
+        "$resolved_root"/*)
+          is_allowed_cwd=1
+          ;;
+      esac
+    done
+
+    if [ "''${#resolved_roots[@]}" -eq 0 ]; then
+      echo "Denied: no valid existing project roots are configured for user '$user_name'." >&2
+      if [ "''${#skipped_roots[@]}" -gt 0 ]; then
+        echo "Configured but missing roots:" >&2
+        for root in "''${skipped_roots[@]}"; do
+          echo "  - $root" >&2
+        done
+      fi
+      exit 1
+    fi
+
+    if [ "$is_allowed_cwd" -ne 1 ]; then
+      echo "Denied: '$cwd_real' is outside allowed project roots for user '$user_name'." >&2
+      echo "Allowed roots:" >&2
+      for root in "''${resolved_roots[@]}"; do
+        echo "  - $root" >&2
+      done
+      exit 1
+    fi
+
+    exec /run/wrappers/bin/sudo --non-interactive \
+      ${runner}/bin/${cfg.wrapper.runnerName} \
+      "$user_name" "$cwd_real" \
+      "TERM=$TERM" "LANG=$LANG" "LC_ALL=''${LC_ALL:-}" "LC_CTYPE=''${LC_CTYPE:-}" "COLORTERM=''${COLORTERM:-}" "TERM_PROGRAM=''${TERM_PROGRAM:-}" \
+      "$@"
+  ''

modules/nixos/pi-agent.nix

@@ -0,0 +1,295 @@
+# NixOS Module for isolated Pi execution (fresh design)
+#
+# Goals:
+# - Dedicated isolated runtime identity (pi-agent user/group)
+# - Host UX via `pi` wrapper command
+# - Per-host-user project allowlists (different roots per user)
+# - No container mode
+# - Merge user Pi config + Nix-managed settings/env into isolated runtime
+{
+  config,
+  lib,
+  pkgs,
+  ...
+}:
+with lib; let
+  cfg = config.m3ta.pi-agent;
+
+  hostUserNames = attrNames cfg.hostUsers;
+
+  runner = import ./pi-agent-runner.nix {inherit cfg pkgs lib;};
+  wrapper = import ./pi-agent-wrapper.nix {inherit cfg pkgs lib runner;};
+in {
+  options.m3ta.pi-agent = {
+    enable = mkEnableOption "isolated Pi execution with dedicated system user and policy-enforced wrapper";
+
+    package = mkOption {
+      type = types.package;
+      default = pkgs.pi-coding-agent;
+      defaultText = literalExpression "pkgs.pi-coding-agent";
+      description = "Pi package providing the executable used in isolated runtime.";
+    };
+
+    binaryName = mkOption {
+      type = types.str;
+      default = "pi-agent";
+      description = "Preferred executable name inside `${cfg.package}/bin` (falls back to pi/pi-agent auto-detection).";
+      example = "pi";
+    };
+
+    user = mkOption {
+      type = types.str;
+      default = "pi-agent";
+      description = "System user that executes Pi in isolated mode.";
+    };
+
+    group = mkOption {
+      type = types.str;
+      default = "pi-agent";
+      description = "System group for the isolated Pi user.";
+    };
+
+    stateDir = mkOption {
+      type = types.str;
+      default = "/var/lib/pi-agent";
+      description = "Writable state/home directory for isolated Pi runtime.";
+    };
+
+    createUser = mkOption {
+      type = types.bool;
+      default = true;
+      description = "Whether to create the dedicated Pi user/group automatically.";
+    };
+
+    hostUsers = mkOption {
+      type = types.attrsOf (types.submodule {
+        options = {
+          projectRoots = mkOption {
+            type = types.listOf types.str;
+            default = [];
+            description = ''
+              Allowed project roots for this host user.
+              `~` and `~/...` are expanded relative to that host user's home.
+            '';
+            example = ["~/p" "~/work/client-a"];
+          };
+
+          configPath = mkOption {
+            type = types.nullOr types.str;
+            default = null;
+            description = ''
+              Optional host path for this user's Pi config source. If null,
+              wrapper.hostConfigPath is used. Relative paths resolve from the
+              host user's home.
+            '';
+            example = ".pi/agent";
+          };
+        };
+      });
+      default = {};
+      description = ''
+        Per-host-user policy map. Keys are host usernames.
+        Each user defines their own allowed project roots and optional config source.
+      '';
+      example = literalExpression ''
+        {
+          m3tam3re = {
+            projectRoots = [ "~/p" "~/src/private" ];
+            configPath = ".pi/agent";
+          };
+          teammate = {
+            projectRoots = [ "~/projects" ];
+          };
+        }
+      '';
+    };
+
+    settings = mkOption {
+      type = types.attrsOf types.anything;
+      default = {};
+      description = ''
+        Nix-managed Pi settings merged into isolated `${cfg.stateDir}/.pi/agent/settings.json`.
+        Merge precedence: synced host settings first, Nix-managed values override recursively.
+      '';
+      example = literalExpression ''
+        {
+          defaultModel = "anthropic/claude-sonnet-4";
+          defaultProvider = "anthropic";
+          quietStartup = true;
+        }
+      '';
+    };
+
+    environment = mkOption {
+      type = types.attrsOf types.str;
+      default = {};
+      description = ''
+        Non-secret Nix-managed environment variables appended into isolated
+        `${cfg.stateDir}/.pi/.env` after synced host values.
+      '';
+    };
+
+    environmentFiles = mkOption {
+      type = types.listOf types.str;
+      default = [];
+      description = ''
+        Paths to env files (secrets/tokens) appended to isolated `${cfg.stateDir}/.pi/.env`
+        after `environment` entries.
+      '';
+    };
+
+    extraPackages = mkOption {
+      type = types.listOf types.package;
+      default = [];
+      description = "Extra packages added to isolated runtime PATH.";
+    };
+
+    projectGroup = mkOption {
+      type = types.nullOr types.str;
+      default = null;
+      description = ''
+        When set, the pi-agent user is added to this group and the group is
+        passed as SupplementaryGroups to the systemd-run sandbox. This allows
+        pi-agent to write to project directories that grant group write access.
+        The user must ensure project directories have appropriate group ownership
+        and permissions (e.g. setgid + group write).
+      '';
+      example = "users";
+    };
+
+    wrapper = {
+      enable = mkOption {
+        type = types.bool;
+        default = true;
+        description = "Enable host-side wrapper command that enforces policy and runs isolated Pi.";
+      };
+
+      commandName = mkOption {
+        type = types.str;
+        default = "pi";
+        description = "Host wrapper command name.";
+      };
+
+      runnerName = mkOption {
+        type = types.str;
+        default = "m3ta-pi-agent-runner";
+        description = "Privileged runner command invoked via scoped sudo rule.";
+      };
+
+      hideDirectBinary = mkOption {
+        type = types.bool;
+        default = true;
+        description = ''
+          When true and wrapper is enabled, do not add the raw Pi package to host PATH,
+          reducing bypass risk by making wrapper the canonical entrypoint.
+        '';
+      };
+
+      syncConfigFromHost = mkOption {
+        type = types.bool;
+        default = true;
+        description = ''
+          Sync host Pi config directory into isolated `${cfg.stateDir}/.pi/agent`
+          on each invocation.
+        '';
+      };
+
+      hostConfigPath = mkOption {
+        type = types.str;
+        default = ".pi/agent";
+        description = ''
+          Default source path for host Pi config sync. Relative paths resolve from
+          the invoking user's home. Per-user hostUsers.<name>.configPath overrides this.
+        '';
+      };
+
+      extraRunArgs = mkOption {
+        type = types.listOf types.str;
+        default = [];
+        description = "Extra arguments inserted before user-provided Pi args.";
+      };
+
+      extraEnvironment = mkOption {
+        type = types.attrsOf types.str;
+        default = {};
+        description = "Additional environment variables passed to isolated Pi runtime.";
+      };
+    };
+  };
+
+  config = mkIf cfg.enable {
+    assertions =
+      [
+        {
+          assertion = cfg.hostUsers != {};
+          message = "m3ta.pi-agent.hostUsers must define at least one authorized host user.";
+        }
+        {
+          assertion = (!cfg.wrapper.enable) || (cfg.hostUsers != {});
+          message = "m3ta.pi-agent.hostUsers must not be empty when wrapper is enabled.";
+        }
+      ]
+      ++ mapAttrsToList (user: userCfg: {
+        assertion = userCfg.projectRoots != [];
+        message = "m3ta.pi-agent.hostUsers.${user}.projectRoots must not be empty.";
+      })
+      cfg.hostUsers;
+
+    users.groups = mkIf cfg.createUser {
+      "${cfg.group}" = {};
+    };
+
+    users.users = mkIf cfg.createUser {
+      "${cfg.user}" = {
+        isSystemUser = true;
+        group = cfg.group;
+        extraGroups = mkIf (cfg.projectGroup != null) [cfg.projectGroup];
+        description = "Isolated Pi agent user";
+        home = cfg.stateDir;
+        createHome = true;
+        shell = pkgs.bashInteractive;
+      };
+    };
+
+    systemd.tmpfiles.rules = [
+      "d ${cfg.stateDir} 0750 ${cfg.user} ${cfg.group} - -"
+      "d ${cfg.stateDir}/.pi 0750 ${cfg.user} ${cfg.group} - -"
+      "d ${cfg.stateDir}/.pi/agent 0750 ${cfg.user} ${cfg.group} - -"
+      "d ${cfg.stateDir}/.pi/agent/sessions 0750 ${cfg.user} ${cfg.group} - -"
+      "d ${cfg.stateDir}/.project-mounts 0750 ${cfg.user} ${cfg.group} - -"
+      "d ${cfg.stateDir}/projects 0750 ${cfg.user} ${cfg.group} - -"
+      "d ${cfg.stateDir}/.npm 0750 ${cfg.user} ${cfg.group} - -"
+      "d ${cfg.stateDir}/.npm-global 0750 ${cfg.user} ${cfg.group} - -"
+      "d ${cfg.stateDir}/.npm-global/bin 0750 ${cfg.user} ${cfg.group} - -"
+      "d ${cfg.stateDir}/.npm-global/lib 0750 ${cfg.user} ${cfg.group} - -"
+    ];
+
+    # Ensure correct ownership of stateDir after user creation.
+    # createHome = true causes useradd to create the directory as root:root
+    # before systemd-tmpfiles can set the intended owner.
+    system.activationScripts.pi-agent-chown = {
+      deps = ["users"];
+      text = ''
+        chown ${cfg.user}:${cfg.group} ${cfg.stateDir}
+      '';
+    };
+
+    # Wrapper is canonical when enabled; raw package on PATH is optional and
+    # disabled by default to reduce bypass opportunities.
+    environment.systemPackages =
+      optional cfg.wrapper.enable wrapper
+      ++ optional ((!cfg.wrapper.enable) || (!cfg.wrapper.hideDirectBinary)) cfg.package;
+
+    security.sudo.extraRules = mkIf (cfg.wrapper.enable && hostUserNames != []) [
+      {
+        users = hostUserNames;
+        commands = [
+          {
+            command = "${runner}/bin/${cfg.wrapper.runnerName}";
+            options = ["NOPASSWD"];
+          }
+        ];
+      }
+    ];
+  };
+}

overlays/default.nix

@@ -1,9 +1,6 @@
 {inputs, ...}: {
   # This one brings our custom packages from the 'pkgs' directory
-  additions = final: prev:
+  additions = final: prev: (import ../pkgs {pkgs = final;});
-    (import ../pkgs {pkgs = final;})
-    # // (inputs.hyprpanel.overlay final prev)
-    // {rose-pine-hyprcursor = inputs.rose-pine-hyprcursor.packages.${prev.stdenv.hostPlatform.system}.default;};
 
   # This one contains whatever you want to overlay
   # You can change versions, add patches, set compilation flags, anything really.
@@ -16,51 +13,8 @@
       brave = prev.brave.override {
         commandLineArgs = "--password-store=gnome-libsecret";
       };
-
-      # nodejs_24 = inputs.nixpkgs-stable.legacyPackages.${prev.system}.nodejs_24;
-      # paperless-ngx = inputs.nixpkgs-45570c2.legacyPackages.${prev.system}.paperless-ngx;
-      # anytype-heart = inputs.nixpkgs-9e58ed7.legacyPackages.${prev.system}.anytype-heart;
-      # trezord = inputs.nixpkgs-2744d98.legacyPackages.${prev.system}.trezord;
-      # mesa = inputs.nixpkgs-master.legacyPackages.${prev.system}.mesa;
-      # hyprpanel = inputs.hyprpanel.packages.${prev.system}.default.overrideAttrs (prev: {
-      #   version = "latest"; # or whatever version you want
-      #   src = final.fetchFromGitHub {
-      #     owner = "Jas-SinghFSU";
-      #     repo = "HyprPanel";
-      #     rev = "master"; # or a specific commit hash
-      #     hash = "sha256-l623fIVhVCU/ylbBmohAtQNbK0YrWlEny0sC/vBJ+dU=";
-      #   };
-      # });
     };
 
-  temp-packages = final: _prev: {
-    temp = import inputs.nixpkgs-9e9486b {
-      system = final.stdenv.hostPlatform.system;
-      config.allowUnfree = true;
-    };
-  };
-
-  stable-packages = final: _prev: {
-    stable = import inputs.nixpkgs-stable {
-      system = final.stdenv.hostPlatform.system;
-      config.allowUnfree = true;
-    };
-  };
-
-  pinned-packages = final: _prev: {
-    pinned = import inputs.nixpkgs-9472de4 {
-      system = final.stdenv.hostPlatform.system;
-      config.allowUnfree = true;
-    };
-  };
-
-  locked-packages = final: _prev: {
-    locked = import inputs.nixpkgs-locked {
-      system = final.stdenv.hostPlatform.system;
-      config.allowUnfree = true;
-    };
-  };
-
   master-packages = final: _prev: {
     master = import inputs.nixpkgs-master {
       system = final.stdenv.hostPlatform.system;

overlays/mods/default.nix

@@ -2,9 +2,6 @@
   # Package modifications
   # This overlay contains package overrides and modifications
 
-  # n8n = import ./n8n.nix {inherit prev;};
-  # beads = import ./beads.nix {inherit prev;};
-
   # Add more modifications here as needed
   # example-package = prev.example-package.override { ... };
 }

pkgs/default.nix

@@ -3,6 +3,7 @@
   inputs,
   ...
 }: let
+  # Used only for flake input pass-throughs (basecamp, openspec, opencode-desktop)
   system = pkgs.stdenv.hostPlatform.system;
 in {
   # Custom packages registry

pkgs/eigent/default.nix

@@ -8,10 +8,10 @@
   nix-update-script,
 }: let
   pname = "eigent";
-  version = "0.0.89";
+  version = "0.0.90";
   src = fetchurl {
     url = "https://github.com/eigent-ai/eigent/releases/download/v${version}/Eigent-${version}.AppImage";
-    hash = "sha256-9KuiFjegfXhCu1W/FCinWX4ae/DsNPudeBcXFfW18Hc=";
+    hash = "sha256-mwCBx+D6mgGqQa8bDuUpo3h49EwFVkwasJwaYc6aXFE=";
   };
   appimageContents = appimageTools.extractType2 {inherit pname version src;};
 in

pkgs/n8n/default.nix

@@ -25,20 +25,20 @@
 in
   stdenv.mkDerivation (finalAttrs: {
     pname = "n8n";
-    version = "stable";
+    version = "2.14.2";
 
     src = fetchFromGitHub {
       owner = "n8n-io";
       repo = "n8n";
-      tag = "${finalAttrs.version}";
+      tag = "n8n@${finalAttrs.version}";
-      hash = "sha256-/atba0ymCqhh5Rt61UxwC2xf8SGrRsEKtlsDCIkg37Y=";
+      hash = "sha256-nWV3DFDkBlfDdoOxwYB0HSrTyKpTt70YxAQYUPartkE=";
     };
 
     pnpmDeps = fetchPnpmDeps {
       inherit (finalAttrs) pname version src;
       pnpm = pnpm_10;
       fetcherVersion = 3;
-      hash = "sha256-YGplNNvIOIY1BthWmejAzucXujq8AkgPJus774GmWCA=";
+      hash = "sha256-0SnPF3CgIja3M1ubLrwyFcx7vY0eHz9DEgn/gDLXN80=";
     };
 
     nativeBuildInputs =

pkgs/opencode-desktop/default.nix

@@ -31,7 +31,7 @@
   # Upstream is missing outputHashes for git dependencies
   # Also fix stale npm deps hash in upstream node_modules FOD
   fixedNodeModules = opencode.node_modules.overrideAttrs {
-    outputHash = "sha256-LRhPPrOKCGUSCEWTpAxPdWKTKVNkg82WrvD25cP3jts=";
+    outputHash = "sha256-285KZ7rZLRoc6XqCZRHc25NE+mmpGh/BVeMpv8aPQtQ=";
   };
 
   opencode-desktop = rustPlatform.buildRustPackage (finalAttrs: {

tests/lib/agents-test.nix

@@ -0,0 +1,26 @@
+let
+  lib = import <nixpkgs/lib>;
+  agentsLib = (import ../../lib {inherit lib;}).agents;
+
+  # Test 1: renderForTool throws for unknown tools
+  testUnknownTool = let
+    result = builtins.tryEval (
+      agentsLib.renderForTool {
+        pkgs = {};
+        agentsInput = {};
+        tool = "unknown-tool";
+      }
+    );
+  in
+    assert result.success == false; {result = "pass";};
+
+  # Test 2: loadCanonical extracts loadAgents from input
+  testLoadCanonical = let
+    fakeInput = {lib.loadAgents = {test = {description = "test";};};};
+    result = agentsLib.loadCanonical {agentsInput = fakeInput;};
+  in
+    assert result == {test = {description = "test";};}; {result = "pass";};
+in {
+  unknown-tool-throws = testUnknownTool;
+  load-canonical = testLoadCanonical;
+}

tests/lib/coding-rules-test.nix

@@ -0,0 +1,48 @@
+let
+  lib = import <nixpkgs/lib>;
+  codingRulesLib = (import ../../lib {inherit lib;}).coding-rules;
+
+  # Test 1: instructions are generated correctly with custom rulesDir
+  testInstructions = let
+    rules = codingRulesLib.mkCodingRules {
+      agents = "/tmp/fake-agents";
+      languages = ["python"];
+      concerns = ["naming"];
+      rulesDir = ".coding-rules";
+    };
+  in
+    assert rules.instructions
+    == [
+      ".coding-rules/concerns/naming.md"
+      ".coding-rules/languages/python.md"
+    ]; {result = "pass";};
+
+  # Test 2: default rulesDir is .opencode-rules
+  testDefaultRulesDir = let
+    rules = codingRulesLib.mkCodingRules {
+      agents = "/tmp/fake-agents";
+    };
+    hasCorrectPrefix = builtins.all (s: builtins.substring 0 15 s == ".opencode-rules") rules.instructions;
+  in
+    assert hasCorrectPrefix == true; {result = "pass";};
+
+  # Test 3: backward-compat alias exists
+  testBackwardCompat = assert codingRulesLib.mkOpencodeRules == codingRulesLib.mkCodingRules; {result = "pass";};
+
+  # Test 4: shellHook contains both the symlink command and the config generation
+  testShellHook = let
+    rules = codingRulesLib.mkCodingRules {
+      agents = "/tmp/fake-agents";
+    };
+    hook = rules.shellHook;
+    hasSymlink = builtins.match ".*ln -sfn.*" hook != null;
+    hasConfigGen = builtins.match ".*coding-rules.json.*" hook != null;
+  in
+    assert hasSymlink;
+    assert hasConfigGen; {result = "pass";};
+in {
+  instructions-correct = testInstructions;
+  default-rules-dir = testDefaultRulesDir;
+  backward-compat = testBackwardCompat;
+  shell-hook = testShellHook;
+}

tests/lib/default.nix

@@ -0,0 +1,4 @@
+{
+  coding-rules = import ./coding-rules-test.nix;
+  agents = import ./agents-test.nix;
+}