fix: pi permissions

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

@@ -7,9 +7,7 @@
 with lib; let
   cfg = config.coding.agents.pi;
   mcpCfg = config.programs.mcp or null;
-
   hasPiPackage = pkgs ? pi;
-
   defaultPiImageArchive =
     if hasPiPackage
     then
@@ -43,30 +41,29 @@ with lib; let
 in {
   options.coding.agents.pi = {
     enable = mkEnableOption "Pi agent management via canonical agent.toml definitions";
-
     container = mkOption {
       description = "Run Pi through a rootless Podman container while keeping a native host UX.";
       default = {};
       type = types.submodule {
         options = {
           enable = mkEnableOption "Containerized Pi wrapper";
-
           name = mkOption {
             type = types.str;
             default = "pi-agent";
             description = "Container name used by the Pi wrapper.";
           };
-
           image = mkOption {
             type = types.str;
-            default = if hasPiPackage then "pi-agent:latest" else "docker.io/nixos/nix:latest";
+            default =
+              if hasPiPackage
+              then "pi-agent:latest"
+              else "docker.io/nixos/nix:latest";
             description = ''
               Podman image to run for Pi.
               Defaults to a local declarative Pi-ready image when `pkgs.pi` exists,
               otherwise falls back to docker.io/nixos/nix:latest.
             '';
           };
-
           imageArchive = mkOption {
             type = types.nullOr types.path;
             default = defaultPiImageArchive;
@@ -76,7 +73,6 @@ in {
               generated when `pkgs.pi` is available.
             '';
           };
-
           projectRoots = mkOption {
             type = types.listOf types.str;
             default = [];
@@ -86,13 +82,11 @@ in {
             '';
             example = ["/home/m3tam3re/p"];
           };
-
           autoStart = mkOption {
             type = types.bool;
             default = true;
             description = "Automatically start container when wrapper is invoked and it is not running.";
           };
-
           autoNixDevelop = mkOption {
             type = types.bool;
             default = false;
@@ -102,13 +96,11 @@ in {
               inside the container.
             '';
           };
-
           extraRunArgs = mkOption {
             type = types.listOf types.str;
             default = [];
             description = "Additional Podman create args appended after safe defaults.";
           };
-
           extraEnv = mkOption {
             type = types.attrsOf types.str;
             default = {};
@@ -117,10 +109,12 @@ in {
         };
       };
     };
-
     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).
@@ -128,7 +122,6 @@ in {
         Automatically inherits from config.programs.mcp.servers.
       '';
     };
-
     agentsInput = mkOption {
       type = types.nullOr types.anything;
       default = null;
@@ -138,7 +131,6 @@ in {
         all agents are listed in AGENTS.md, and subagent .md files are deployed.
       '';
     };
-
     modelOverrides = mkOption {
       type = types.attrsOf types.str;
       default = {};
@@ -148,7 +140,6 @@ in {
           { chiron = "anthropic/claude-sonnet-4"; chiron-forge = "anthropic/claude-sonnet-4"; }
       '';
     };
-
     primaryAgent = mkOption {
       type = types.nullOr types.str;
       default = null;
@@ -157,7 +148,6 @@ in {
         When null, the first agent with mode="primary" is used.
       '';
     };
-
     settings = mkOption {
       type = types.submodule {
         freeformType = types.attrsOf types.anything;
@@ -170,43 +160,36 @@ in {
               These are written to ~/.pi/agent/settings.json.
             '';
           };
-
           defaultProvider = mkOption {
             type = types.nullOr types.str;
             default = null;
             description = "Default LLM provider (e.g. 'anthropic', 'openai', 'zai').";
           };
-
           defaultModel = mkOption {
             type = types.nullOr types.str;
             default = null;
             description = "Default model ID.";
           };
-
           defaultThinkingLevel = mkOption {
             type = types.nullOr (types.enum ["off" "minimal" "low" "medium" "high" "xhigh"]);
             default = null;
             description = "Default extended thinking level.";
           };
-
           theme = mkOption {
             type = types.nullOr types.str;
             default = null;
             description = "Pi theme name.";
           };
-
           hideThinkingBlock = mkOption {
             type = types.nullOr types.bool;
             default = null;
             description = "Hide thinking blocks in output.";
           };
-
           quietStartup = mkOption {
             type = types.nullOr types.bool;
             default = null;
             description = "Hide startup header.";
           };
-
           compaction = mkOption {
             type = types.nullOr (types.submodule {
               options = {
@@ -227,25 +210,21 @@ in {
             default = null;
             description = "Auto-compaction settings.";
           };
-
           enabledModels = mkOption {
             type = types.nullOr (types.listOf types.str);
             default = null;
             description = "Model patterns for Ctrl+P cycling.";
           };
-
           sessionDir = mkOption {
             type = types.nullOr types.str;
             default = null;
             description = "Directory where session files are stored.";
           };
-
           extensions = mkOption {
             type = types.listOf types.str;
             default = [];
             description = "Local extension file paths or directories.";
           };
-
           skills = mkOption {
             type = types.listOf types.str;
             default = [];
@@ -261,7 +240,6 @@ in {
       '';
     };
   };
-
   config = mkIf cfg.enable (let
     # Build settings.json by filtering out null values recursively
     filterNulls = attrs:
@@ -271,12 +249,13 @@ 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;
-
     projectRoots = map toString cfg.container.projectRoots;
     projectRootsShell = concatStringsSep " " (map escapeShellArg projectRoots);
     extraRunArgsShell = concatStringsSep " " (map escapeShellArg cfg.container.extraRunArgs);
@@ -288,39 +267,44 @@ in {
       if cfg.container.imageArchive != null
       then escapeShellArg (toString cfg.container.imageArchive)
       else "";
-
     piWrapper = pkgs.writeShellScriptBin "pi" ''
       set -euo pipefail
-
       PODMAN="${pkgs.podman}/bin/podman"
       REALPATH="${pkgs.coreutils}/bin/realpath"
-
       CONTAINER_NAME=${escapeShellArg cfg.container.name}
       IMAGE=${escapeShellArg cfg.container.image}
       IMAGE_ARCHIVE=${imageArchiveShell}
-      AUTO_START=${if cfg.container.autoStart then "1" else "0"}
+      AUTO_START=${
-      AUTO_NIX_DEVELOP=${if cfg.container.autoNixDevelop then "1" else "0"}
+        if cfg.container.autoStart
+        then "1"
+        else "0"
+      }
+      AUTO_NIX_DEVELOP=${
+        if cfg.container.autoNixDevelop
+        then "1"
+        else "0"
+      }
       HOST_PI_DIR=${hostPiDirShell}
-
+      PI_CONFIG_MOUNT="/pi-config"
+      WRAPPER_SCHEMA_VERSION="4"
+      RUNTIME_HOME="/tmp"
+      RUNTIME_NPM_PREFIX="/tmp/.npm-global"
+      RUNTIME_NPM_CACHE="/tmp/.npm-cache"
+      RUNTIME_TMPDIR="/tmp/.runtime-tmp"
       PROJECT_ROOTS=(${projectRootsShell})
       EXTRA_RUN_ARGS=(${extraRunArgsShell})
       EXTRA_ENV_VARS=(${extraEnvShell})
-
       err() {
         printf "pi-wrapper: %s\n" "$1" >&2
         exit 1
       }
-
       if [ "''${#PROJECT_ROOTS[@]}" -eq 0 ]; then
         err "No allowed projectRoots configured. Set coding.agents.pi.container.projectRoots."
       fi
-
       if ! command -v "$PODMAN" >/dev/null 2>&1; then
         err "podman binary not found at $PODMAN"
       fi
-
       CWD="$($REALPATH -m "$PWD")"
-
       cwd_allowed=0
       NORMALIZED_ROOTS=()
       for root in "''${PROJECT_ROOTS[@]}"; do
@@ -332,7 +316,6 @@ in {
             ;;
         esac
       done
-
       if [ "$cwd_allowed" -ne 1 ]; then
         {
           printf "pi-wrapper: cwd '%s' is outside allowed projectRoots.\n" "$CWD"
@@ -343,88 +326,96 @@ in {
         } >&2
         exit 1
       fi
-
       tty_args=()
       if [ -t 0 ] && [ -t 1 ]; then
         tty_args=(-it)
       fi
-
       ensure_image_available() {
         if [ -n "$IMAGE_ARCHIVE" ] && [ -f "$IMAGE_ARCHIVE" ]; then
           "$PODMAN" load -i "$IMAGE_ARCHIVE" >/dev/null
         fi
-
         if ! "$PODMAN" image exists "$IMAGE"; then
           err "Container image '$IMAGE' is not available and no valid imageArchive was provided."
         fi
       }
-
       create_container() {
         mount_args=()
-
         for root in "''${NORMALIZED_ROOTS[@]}"; do
           mount_args+=("-v" "$root:$root:rw")
         done
-
         if [ ! -S /nix/var/nix/daemon-socket/socket ]; then
           err "Host Nix daemon socket not found at /nix/var/nix/daemon-socket/socket"
         fi
-
         mount_args+=("-v" "/nix/var/nix/daemon-socket/socket:/nix/var/nix/daemon-socket/socket:rw")
-
         mkdir -p "$HOST_PI_DIR"
-        mount_args+=("-v" "$HOST_PI_DIR:/tmp/.pi:rw")
+        mount_args+=("-v" "$HOST_PI_DIR:$PI_CONFIG_MOUNT:rw")
-
         if [ -d /nix/store ]; then
           mount_args+=("-v" "/nix/store:/nix/store:ro")
         fi
-
         if [ -e /etc/nix/nix.conf ]; then
           mount_args+=("-v" "/etc/nix/nix.conf:/etc/nix/nix.conf:ro")
         fi
-
         if [ -d /etc/ssl/certs ]; then
           mount_args+=("-v" "/etc/ssl/certs:/etc/ssl/certs:ro")
         fi
-
         if [ -d /etc/pki ]; then
           mount_args+=("-v" "/etc/pki:/etc/pki:ro")
         fi
-
         env_args=()
         for kv in "''${EXTRA_ENV_VARS[@]}"; do
           env_args+=("--env" "$kv")
         done
-
         "$PODMAN" create \
           --name "$CONTAINER_NAME" \
           --hostname "$CONTAINER_NAME" \
+          --label io.m3ta.pi-wrapper-version="$WRAPPER_SCHEMA_VERSION" \
           --userns keep-id \
           --user "$(${pkgs.coreutils}/bin/id -u):$(${pkgs.coreutils}/bin/id -g)" \
           --security-opt no-new-privileges \
           --workdir /tmp \
-          --tmpfs /tmp:rw,nodev,nosuid \
+          --tmpfs /tmp:rw,nodev,nosuid,mode=1777 \
-          --env HOME=/tmp \
+          --env HOME="$RUNTIME_HOME" \
+          --env PI_CODING_AGENT_DIR="$PI_CONFIG_MOUNT/agent" \
           --env NIX_REMOTE=daemon \
-          --env NPM_CONFIG_PREFIX=/tmp/.npm-global \
+          --env TMPDIR="$RUNTIME_TMPDIR" \
-          --env npm_config_prefix=/tmp/.npm-global \
+          --env NPM_CONFIG_PREFIX="$RUNTIME_NPM_PREFIX" \
-          --env NPM_CONFIG_CACHE=/tmp/.npm \
+          --env npm_config_prefix="$RUNTIME_NPM_PREFIX" \
-          --env npm_config_cache=/tmp/.npm \
+          --env NPM_CONFIG_CACHE="$RUNTIME_NPM_CACHE" \
-          --env PATH=/tmp/.npm-global/bin:/bin:/usr/bin \
+          --env npm_config_cache="$RUNTIME_NPM_CACHE" \
+          --env PATH="$RUNTIME_NPM_PREFIX/bin:/bin:/usr/bin" \
           "''${mount_args[@]}" \
           "''${env_args[@]}" \
           "''${EXTRA_RUN_ARGS[@]}" \
           "$IMAGE" \
           sleep infinity >/dev/null
       }
-
+      runtime_env_args=(
+        --env "HOME=$RUNTIME_HOME"
+        --env "PI_CODING_AGENT_DIR=$PI_CONFIG_MOUNT/agent"
+        --env NIX_REMOTE=daemon
+        --env "TMPDIR=$RUNTIME_TMPDIR"
+        --env "NPM_CONFIG_PREFIX=$RUNTIME_NPM_PREFIX"
+        --env "npm_config_prefix=$RUNTIME_NPM_PREFIX"
+        --env "NPM_CONFIG_CACHE=$RUNTIME_NPM_CACHE"
+        --env "npm_config_cache=$RUNTIME_NPM_CACHE"
+        --env "PATH=$RUNTIME_NPM_PREFIX/bin:/bin:/usr/bin"
+      )
+      recreate_container() {
+        "$PODMAN" rm -f "$CONTAINER_NAME" >/dev/null 2>&1 || true
+        ensure_image_available
+        create_container
+      }
       ensure_container_running() {
         if ! "$PODMAN" container exists "$CONTAINER_NAME"; then
           ensure_image_available
           create_container
+        else
+          schema_version="$("$PODMAN" inspect -f '{{ index .Config.Labels "io.m3ta.pi-wrapper-version" }}' "$CONTAINER_NAME" 2>/dev/null || true)"
+          if [ "$schema_version" != "$WRAPPER_SCHEMA_VERSION" ]; then
+            recreate_container
+          fi
         fi
-
+        running="$("$PODMAN" inspect -f '{{.State.Running}}' "$CONTAINER_NAME" 2>/dev/null || true)"
-        running="$($PODMAN inspect -f '{{.State.Running}}' "$CONTAINER_NAME" 2>/dev/null || true)"
         if [ "$running" != "true" ]; then
           if [ "$AUTO_START" = "1" ]; then
             "$PODMAN" start "$CONTAINER_NAME" >/dev/null
@@ -433,20 +424,24 @@ in {
           fi
         fi
       }
-
+      ensure_runtime_dirs() {
+        if ! "$PODMAN" exec "''${runtime_env_args[@]}" --workdir /tmp "$CONTAINER_NAME" sh -lc 'mkdir -p "$NPM_CONFIG_PREFIX" "$NPM_CONFIG_CACHE" "$TMPDIR"'; then
+          err "Failed to prepare writable npm runtime directories in container '$CONTAINER_NAME'."
+        fi
+        if ! "$PODMAN" exec "''${runtime_env_args[@]}" --workdir /tmp "$CONTAINER_NAME" sh -lc 'test -w "$NPM_CONFIG_PREFIX" && test -w "$NPM_CONFIG_CACHE" && test -w "$TMPDIR"'; then
+          err "Container runtime dirs are not writable for npm. Remove stale container with: podman rm -f $CONTAINER_NAME"
+        fi
+      }
       ensure_container_running
-
+      ensure_runtime_dirs
       if [ "$AUTO_NIX_DEVELOP" = "1" ] && [ -f "$CWD/flake.nix" ]; then
-        exec "$PODMAN" exec "''${tty_args[@]}" --workdir "$CWD" "$CONTAINER_NAME" nix develop -c pi "$@"
+        exec "$PODMAN" exec "''${tty_args[@]}" "''${runtime_env_args[@]}" --workdir "$CWD" "$CONTAINER_NAME" nix develop -c pi "$@"
       fi
-
+      if "$PODMAN" exec "''${runtime_env_args[@]}" --workdir "$CWD" "$CONTAINER_NAME" sh -lc 'command -v pi >/dev/null 2>&1'; then
-      if "$PODMAN" exec --workdir "$CWD" "$CONTAINER_NAME" sh -lc 'command -v pi >/dev/null 2>&1'; then
+        exec "$PODMAN" exec "''${tty_args[@]}" "''${runtime_env_args[@]}" --workdir "$CWD" "$CONTAINER_NAME" pi "$@"
-        exec "$PODMAN" exec "''${tty_args[@]}" --workdir "$CWD" "$CONTAINER_NAME" pi "$@"
       fi
-
       err "Container '$CONTAINER_NAME' does not have 'pi' in PATH (image: $IMAGE). Use a Pi-ready image or run from a flake project with autoNixDevelop=true."
     '';
-
     # Rendered agents (only computed when agentsInput is set)
     rendered =
       if cfg.agentsInput != null
@@ -458,23 +453,20 @@ in {
           primaryAgent = cfg.primaryAgent;
         }
       else null;
-
     # Dynamic home.file entries for agent .md files
     agentFiles =
       if cfg.agentsInput != null
-      then
+      then let
-        let
+        agentNames = builtins.attrNames cfg.agentsInput.lib.loadAgents;
-          agentNames = builtins.attrNames cfg.agentsInput.lib.loadAgents;
+      in
-        in
+        builtins.listToAttrs (
-          builtins.listToAttrs (
+          map (name: {
-            map (name: {
+            name = ".pi/agent/agents/${name}.md";
-              name = ".pi/agent/agents/${name}.md";
+            value = {text = builtins.readFile "${rendered}/agents/${name}.md";};
-              value = {text = builtins.readFile "${rendered}/agents/${name}.md";};
+          })
-            })
+          agentNames
-            agentNames
+        )
-          )
       else {};
-
     skillsSource =
       if cfg.agentsInput != null
       then
@@ -499,49 +491,52 @@ in {
         assertion = all (path: hasPrefix "/" (toString path)) cfg.container.projectRoots;
         message = "coding.agents.pi.container.projectRoots entries must be absolute paths.";
       };
-
     home.packages =
       (optional cfg.container.enable piWrapper)
       ++ (optional (!cfg.container.enable && hasPiPackage) pkgs.pi);
-
     home.file = mkMerge [
       # ── MCP servers from programs.mcp → ~/.pi/agent/mcp.json ───────
       (mkIf (cfg.mcpServers != {}) {
         ".pi/agent/mcp.json".text = builtins.toJSON {mcpServers = cfg.mcpServers;};
       })
-
       # ── ~/.pi/agent/settings.json ──────────────────────────────────
       {
         ".pi/agent/settings.json".text = builtins.toJSON piSettings;
       }
-
       # ── AGENTS.md — agent descriptions and specialist listing ──────
       (mkIf (cfg.agentsInput != null) {
         ".pi/agent/AGENTS.md".text = builtins.readFile "${rendered}/AGENTS.md";
       })
-
       # ── SYSTEM.md — primary agent's system prompt ──────────────────
       (mkIf (cfg.agentsInput != null) {
         ".pi/agent/SYSTEM.md".text = builtins.readFile "${rendered}/SYSTEM.md";
       })
-
       # ── Agents — pi-subagents .md files ────────────────────────────
       agentFiles
-
       # ── Skills symlinked from AGENTS repo (non-container mode) ─────
       (mkIf (cfg.agentsInput != null && !cfg.container.enable) {
         ".pi/agent/skills".source = skillsSource;
       })
     ];
-
     home.activation.piMaterializeSkills = mkIf (cfg.container.enable && cfg.agentsInput != null) (
       lib.hm.dag.entryAfter ["writeBoundary"] ''
         skillsSrc=${escapeShellArg "${skillsSource}"}
         skillsDst=${escapeShellArg "${config.home.homeDirectory}/.pi/agent/skills"}
-
+        skillsParent="$(${pkgs.coreutils}/bin/dirname "$skillsDst")"
-        ${pkgs.coreutils}/bin/rm -rf "$skillsDst"
+        skillsNew="$skillsParent/.skills-new-$$"
-        ${pkgs.coreutils}/bin/mkdir -p "$skillsDst"
+        skillsOld="$skillsParent/.skills-old-$$"
-        ${pkgs.coreutils}/bin/cp -aL "$skillsSrc"/. "$skillsDst"/
+        ${pkgs.coreutils}/bin/mkdir -p "$skillsParent"
+        ${pkgs.coreutils}/bin/rm -rf "$skillsNew"
+        ${pkgs.coreutils}/bin/mkdir -p "$skillsNew"
+        ${pkgs.coreutils}/bin/cp -aL "$skillsSrc"/. "$skillsNew"/
+        if [ -e "$skillsDst" ]; then
+          ${pkgs.coreutils}/bin/mv "$skillsDst" "$skillsOld"
+        fi
+        ${pkgs.coreutils}/bin/mv "$skillsNew" "$skillsDst"
+        if [ -e "$skillsOld" ]; then
+          ${pkgs.coreutils}/bin/chmod -R u+w "$skillsOld" 2>/dev/null || true
+          ${pkgs.coreutils}/bin/rm -rf "$skillsOld" 2>/dev/null || true
+        fi
       ''
     );
   });