@kynetic-ai/spec 0.1.2 → 0.3.0

package/dist/cli/commands/setup.js

@@ -1,11 +1,45 @@
-import * as fs from 'node:fs/promises';
-import * as path from 'node:path';
-import * as os from 'node:os';
-import * as readline from 'node:readline/promises';
-import { success, error, warn } from '../output.js';
-import { errors } from '../../strings/index.js';
-import { getShadowStatus, repairShadow, getGitRoot, SHADOW_BRANCH_NAME, } from '../../parser/shadow.js';
-import { EXIT_CODES } from '../exit-codes.js';
+/**
+ * Enhanced setup command for kspec agent integration.
+ *
+ * Orchestrates the full onboarding pipeline:
+ * - Detect agent environment (Claude Code, Cline, etc.)
+ * - Install hooks (UserPromptSubmit, Stop, PreToolUse guards)
+ * - Render skills from .kspec/skills/ to .claude/skills/
+ * - Generate kspec-agents.md
+ *
+ * AC: @enhanced-setup ac-1 - summary displayed listing each step performed
+ * AC: @enhanced-setup ac-2 - all hook entries (UserPromptSubmit, Stop, PreToolUse) present
+ * AC: @enhanced-setup ac-3 - rendered skill files exist for each skill targeting claude-code
+ * AC: @enhanced-setup ac-4 - kspec-agents.md exists after setup
+ * AC: @enhanced-setup ac-5 - --skip-skills flag skips skill rendering
+ * AC: @enhanced-setup ac-6 - --dry-run displays planned actions without changes
+ * AC: @enhanced-setup ac-7 - --status reports current state including agent detected
+ * AC: @enhanced-setup ac-8 - --status shows hooks status, skills rendered count, agents.md freshness
+ * AC: @enhanced-setup ac-9 - skills referenced by ralph (task-work, reflect) are present
+ */
+import * as fs from "node:fs/promises";
+import * as os from "node:os";
+import * as path from "node:path";
+import * as readline from "node:readline/promises";
+import chalk from "chalk";
+import { getGitRoot, getShadowStatus, repairShadow, SHADOW_BRANCH_NAME, } from "../../parser/shadow.js";
+import { errors } from "../../strings/index.js";
+import { EXIT_CODES } from "../exit-codes.js";
+import { error, output, success, warn } from "../output.js";
+/**
+ * Log a message at debug level (only when KSPEC_DEBUG=1)
+ * AC: @setup-pipeline-unification ac-4
+ */
+function debugLog(message, detail) {
+    if (process.env.KSPEC_DEBUG === "1") {
+        if (detail) {
+            console.error(`[DEBUG] setup: ${message}`, detail);
+        }
+        else {
+            console.error(`[DEBUG] setup: ${message}`);
+        }
+    }
+}
 /**
  * Detect which agent environment we're running in.
  * Returns the detected agent type and confidence level.
@@ -17,23 +51,29 @@ export function detectAgent() {
     // CLAUDECODE=1 is set in CLI sessions
     // CLAUDE_CODE_ENTRYPOINT indicates entry point (cli, etc.)
     // CLAUDE_PROJECT_DIR is set in some contexts
-    if (process.env.CLAUDECODE === '1' || process.env.CLAUDE_CODE_ENTRYPOINT || process.env.CLAUDE_PROJECT_DIR) {
+    if (process.env.CLAUDECODE === "1" ||
+        process.env.CLAUDE_CODE_ENTRYPOINT ||
+        process.env.CLAUDE_PROJECT_DIR) {
         return {
-            type: 'claude-code',
-            confidence: 'high',
-            configPath: path.join(os.homedir(), '.claude', 'settings.json'),
+            type: "claude-code",
+            confidence: "high",
+            configPath: path.join(os.homedir(), ".claude", "settings.json"),
             envVars: {
                 ...(process.env.CLAUDECODE && { CLAUDECODE: process.env.CLAUDECODE }),
-                ...(process.env.CLAUDE_CODE_ENTRYPOINT && { CLAUDE_CODE_ENTRYPOINT: process.env.CLAUDE_CODE_ENTRYPOINT }),
-                ...(process.env.CLAUDE_PROJECT_DIR && { CLAUDE_PROJECT_DIR: process.env.CLAUDE_PROJECT_DIR }),
+                ...(process.env.CLAUDE_CODE_ENTRYPOINT && {
+                    CLAUDE_CODE_ENTRYPOINT: process.env.CLAUDE_CODE_ENTRYPOINT,
+                }),
+                ...(process.env.CLAUDE_PROJECT_DIR && {
+                    CLAUDE_PROJECT_DIR: process.env.CLAUDE_PROJECT_DIR,
+                }),
             },
         };
     }
     // Cline: CLINE_ACTIVE is set when running in Cline terminal
     if (process.env.CLINE_ACTIVE) {
         return {
-            type: 'cline',
-            confidence: 'high',
+            type: "cline",
+            confidence: "high",
             // Cline uses VS Code settings, but env vars should be in shell profile
             configPath: undefined,
             envVars: { CLINE_ACTIVE: process.env.CLINE_ACTIVE },
@@ -42,63 +82,64 @@ export function detectAgent() {
     // GitHub Copilot CLI: Check for copilot-specific markers
     if (process.env.COPILOT_MODEL || process.env.GH_TOKEN) {
         return {
-            type: 'copilot-cli',
-            confidence: 'medium',
-            configPath: path.join(os.homedir(), '.copilot', 'config.json'),
+            type: "copilot-cli",
+            confidence: "medium",
+            configPath: path.join(os.homedir(), ".copilot", "config.json"),
         };
     }
     // Aider: Check for AIDER_* env vars
     if (process.env.AIDER_MODEL || process.env.AIDER_DARK_MODE !== undefined) {
         return {
-            type: 'aider',
-            confidence: 'high',
-            configPath: path.join(os.homedir(), '.aider.conf.yml'),
+            type: "aider",
+            confidence: "high",
+            configPath: path.join(os.homedir(), ".aider.conf.yml"),
         };
     }
     // OpenCode: Check for OPENCODE_* env vars
     if (process.env.OPENCODE_CONFIG_DIR || process.env.OPENCODE_CONFIG) {
         return {
-            type: 'opencode',
-            confidence: 'high',
-            configPath: process.env.OPENCODE_CONFIG || path.join(os.homedir(), '.config', 'opencode', 'opencode.json'),
+            type: "opencode",
+            confidence: "high",
+            configPath: process.env.OPENCODE_CONFIG ||
+                path.join(os.homedir(), ".config", "opencode", "opencode.json"),
         };
     }
     // Gemini CLI: GEMINI_CLI=1 is set when running in Gemini CLI
-    if (process.env.GEMINI_CLI === '1') {
+    if (process.env.GEMINI_CLI === "1") {
         return {
-            type: 'gemini-cli',
-            confidence: 'high',
-            configPath: path.join(os.homedir(), '.gemini', 'settings.json'),
-            envVars: { GEMINI_CLI: '1' },
+            type: "gemini-cli",
+            confidence: "high",
+            configPath: path.join(os.homedir(), ".gemini", "settings.json"),
+            envVars: { GEMINI_CLI: "1" },
         };
     }
     // Codex CLI: CODEX_SANDBOX is set when running in sandbox
     if (process.env.CODEX_SANDBOX) {
         return {
-            type: 'codex-cli',
-            confidence: 'high',
-            configPath: path.join(os.homedir(), '.codex', 'config.toml'),
+            type: "codex-cli",
+            confidence: "high",
+            configPath: path.join(os.homedir(), ".codex", "config.toml"),
             envVars: { CODEX_SANDBOX: process.env.CODEX_SANDBOX },
         };
     }
     // Amp (Sourcegraph): Check for AMP_API_KEY or AMP_TOOLBOX
     if (process.env.AMP_API_KEY || process.env.AMP_TOOLBOX) {
         return {
-            type: 'amp',
-            confidence: 'medium',
-            configPath: path.join(os.homedir(), '.config', 'amp', 'settings.json'),
+            type: "amp",
+            confidence: "medium",
+            configPath: path.join(os.homedir(), ".config", "amp", "settings.json"),
         };
     }
     return {
-        type: 'unknown',
-        confidence: 'low',
+        type: "unknown",
+        confidence: "low",
     };
 }
 /**
  * Install KSPEC_AUTHOR config for Claude Code (global settings)
  */
 async function installClaudeCodeConfig(author) {
-    const configPath = path.join(os.homedir(), '.claude', 'settings.json');
+    const configPath = path.join(os.homedir(), ".claude", "settings.json");
     const configDir = path.dirname(configPath);
     try {
         // Ensure directory exists
@@ -106,56 +147,255 @@ async function installClaudeCodeConfig(author) {
         // Read existing config or start fresh
         let config = {};
         try {
-            const existing = await fs.readFile(configPath, 'utf-8');
+            const existing = await fs.readFile(configPath, "utf-8");
             config = JSON.parse(existing);
         }
-        catch {
-            // File doesn't exist or invalid JSON, start fresh
+        catch (err) {
+            debugLog("No existing Claude Code config, starting fresh", err);
         }
         // Merge env settings
         const env = config.env || {};
         env.KSPEC_AUTHOR = author;
         config.env = env;
         // Write back
-        await fs.writeFile(configPath, JSON.stringify(config, null, 2) + '\n', 'utf-8');
+        await fs.writeFile(configPath, `${JSON.stringify(config, null, 2)}\n`, "utf-8");
         return true;
     }
     catch (err) {
+        debugLog("Failed to install Claude Code config", err);
         return false;
     }
 }
+/**
+ * PreToolUse guard hook scripts
+ * These are the shell scripts that will be installed to .claude/hooks/
+ */
+const GUARD_SCRIPTS = {
+    "kspec-worktree-guard.sh": `#!/bin/bash
+# Guard against dangerous git operations in .kspec worktree
+#
+# This hook prevents accidentally creating branches or switching
+# branches in the .kspec worktree, which should always stay on kspec-meta.
+
+# Read the tool input from stdin
+INPUT=$(cat)
+
+# Extract the command from the JSON input
+COMMAND=$(echo "$INPUT" | jq -r '.tool_input.command // empty' 2>/dev/null)
+
+# If no command, allow (not a Bash tool call)
+if [ -z "$COMMAND" ]; then
+  echo '{"decision": "allow"}'
+  exit 0
+fi
+
+# Two views of the command for safe matching:
+# 1. UNQUOTED: remove quote chars (keeps content) to catch split-quote
+#    bypasses like: git "reset" --hard → git reset --hard
+# 2. STRIPPED: remove entire quoted strings to ignore patterns in args
+#    like: echo "git reset" → echo
+UNQUOTED=$(echo "$COMMAND" | sed 's/["\\x27]//g')
+STRIPPED=$(echo "$COMMAND" | sed -e "s/\\x27[^\\x27]*\\x27//g" -e 's/"[^"]*"//g')
+# First command word (handles leading whitespace)
+FIRST_CMD=$(echo "$COMMAND" | sed 's/^[[:space:]]*//' | cut -d' ' -f1)
+
+# Block deleting kspec-meta from anywhere (check unquoted to catch bypasses)
+if [[ "$UNQUOTED" == *"git branch -d kspec-meta"* || "$UNQUOTED" == *"git branch -D kspec-meta"* ]]; then
+  cat <<EOF
+{
+  "decision": "block",
+  "reason": "[kspec-worktree-guard] BLOCKED: Cannot delete kspec-meta branch. This is the main branch for the .kspec worktree."
+}
+EOF
+  exit 0
+fi
+
+# Get cwd from hook input (not pwd - hook runs in different context)
+CWD=$(echo "$INPUT" | jq -r '.cwd // empty' 2>/dev/null)
+IN_KSPEC=false
+
+if [[ "$CWD" == *"/.kspec"* || "$CWD" == *"/.kspec" ]]; then
+  IN_KSPEC=true
+fi
+
+# Also check if command contains cd to .kspec
+if [[ "$COMMAND" == *"cd "*".kspec"* || "$COMMAND" == *"cd .kspec"* ]]; then
+  IN_KSPEC=true
+fi
+
+if [ "$IN_KSPEC" = false ]; then
+  echo '{"decision": "allow"}'
+  exit 0
+fi
+
+# Dangerous patterns in .kspec (branch creation/modification/history rewriting)
+# Note: "git checkout kspec-meta" is safe and allowed
+DANGEROUS_PATTERNS=(
+  # Branch creation
+  "git checkout -b"
+  "git checkout -B"
+  "git branch -c"
+  "git branch -C"
+  "git branch -m"
+  "git branch -M"
+  "git switch -c"
+  "git switch -C"
+  "git switch --create"
+  # History rewriting - these can cause conflicts with active sessions
+  "git reset"
+  "git rebase"
+  "git cherry-pick"
+  "git commit --amend"
+  # Force push
+  "git push --force"
+  "git push -f"
+  # Discarding changes
+  "git stash"
+  "git clean"
+  "git checkout -- "
+  "git restore"
+)
+
+for pattern in "\${DANGEROUS_PATTERNS[@]}"; do
+  # Block if:
+  # - Pattern matches UNQUOTED AND first command is "git" (catches split-quote bypasses), OR
+  # - Pattern matches STRIPPED (actual command outside any quotes)
+  # This allows: echo "git reset", grep "git stash" (first cmd is echo/grep, pattern not in STRIPPED)
+  # This blocks: git reset, git "reset" --hard, git st'ash' (first cmd is git OR pattern in STRIPPED)
+  if [[ "$STRIPPED" == *"$pattern"* ]] || { [[ "$UNQUOTED" == *"$pattern"* ]] && [[ "$FIRST_CMD" == "git" ]]; }; then
+    cat <<EOF
+{
+  "decision": "block",
+  "reason": "[kspec-worktree-guard] BLOCKED: Dangerous git operation in .kspec worktree. This worktree contains active session data and must stay on kspec-meta. Operations like reset, rebase, stash, and clean can corrupt session files."
+}
+EOF
+    exit 0
+  fi
+done
+
+# Allow all other commands
+echo '{"decision": "allow"}'
+`,
+    "ralph-task-limit-guard.sh": `#!/bin/bash
+# Ralph task limit guard - blocks task start when limit reached
+#
+# This hook provides hard enforcement of the --max-tasks limit.
+# Ralph writes a marker file when the limit is reached; this hook
+# blocks 'kspec task start' commands when that marker exists.
+
+# Marker file location (relative to project root)
+MARKER_FILE=".claude/ralph-task-limit.json"
+
+# Read the tool input from stdin
+INPUT=$(cat)
+
+# Extract the command from the JSON input
+COMMAND=$(echo "$INPUT" | jq -r '.tool_input.command // empty' 2>/dev/null)
+
+# If no command, allow (not a Bash tool call)
+if [ -z "$COMMAND" ]; then
+  echo '{"decision": "allow"}'
+  exit 0
+fi
+
+# Only check commands that match "kspec task start"
+if [[ ! "$COMMAND" =~ kspec[[:space:]]+task[[:space:]]+start ]]; then
+  echo '{"decision": "allow"}'
+  exit 0
+fi
+
+# Get cwd from hook input to find marker file
+CWD=$(echo "$INPUT" | jq -r '.cwd // empty' 2>/dev/null)
+if [ -z "$CWD" ]; then
+  CWD="$PWD"
+fi
+
+# Find project root by walking up looking for .claude directory
+PROJECT_ROOT="$CWD"
+while [ "$PROJECT_ROOT" != "/" ]; do
+  if [ -d "$PROJECT_ROOT/.claude" ]; then
+    break
+  fi
+  PROJECT_ROOT=$(dirname "$PROJECT_ROOT")
+done
+
+if [ "$PROJECT_ROOT" = "/" ]; then
+  # No .claude directory found, allow
+  echo '{"decision": "allow"}'
+  exit 0
+fi
+
+MARKER_PATH="$PROJECT_ROOT/$MARKER_FILE"
+
+# Check if marker file exists
+if [ ! -f "$MARKER_PATH" ]; then
+  echo '{"decision": "allow"}'
+  exit 0
+fi
+
+# Read marker file and check if active
+ACTIVE=$(jq -r '.active // false' "$MARKER_PATH" 2>/dev/null)
+if [ "$ACTIVE" != "true" ]; then
+  echo '{"decision": "allow"}'
+  exit 0
+fi
+
+# Extract limit info for error message
+MAX=$(jq -r '.max // "?"' "$MARKER_PATH" 2>/dev/null)
+COMPLETED=$(jq -r '.completed // "?"' "$MARKER_PATH" 2>/dev/null)
+
+# Block the command
+cat <<EOF
+{
+  "decision": "block",
+  "reason": "[ralph-task-limit-guard] BLOCKED: Task limit reached (\${COMPLETED}/\${MAX} tasks completed this iteration). This limit was set by --max-tasks. Please wrap up current work and let the iteration end naturally. Do not attempt to start new tasks."
+}
+EOF
+exit 0
+`,
+};
 /**
  * Install hooks to project-level Claude Code settings (.claude/settings.json)
+ * AC: @enhanced-setup ac-2 - all hook entries present
  */
-async function installClaudeCodeHooks(projectDir) {
-    const configPath = path.join(projectDir, '.claude', 'settings.json');
+async function installClaudeCodeHooks(projectDir, dryRun = false) {
+    const configPath = path.join(projectDir, ".claude", "settings.json");
     const configDir = path.dirname(configPath);
-    const result = { stop: false, promptCheck: false };
+    const hooksDir = path.join(projectDir, ".claude", "hooks");
+    const result = {
+        promptCheck: false,
+        stop: false,
+        preToolUse: false,
+        guardsCreated: [],
+    };
     try {
-        // Ensure directory exists
-        await fs.mkdir(configDir, { recursive: true });
+        // Ensure directories exist
+        if (!dryRun) {
+            await fs.mkdir(configDir, { recursive: true });
+            await fs.mkdir(hooksDir, { recursive: true });
+        }
         // Read existing config or start fresh
         let config = {};
         try {
-            const existing = await fs.readFile(configPath, 'utf-8');
+            const existing = await fs.readFile(configPath, "utf-8");
             config = JSON.parse(existing);
         }
-        catch {
-            // File doesn't exist or invalid JSON, start fresh
+        catch (err) {
+            debugLog("No existing hooks config, starting fresh", err);
         }
         // Get or create hooks object
         const hooks = config.hooks || {};
         // Install UserPromptSubmit hook (spec-first reminder)
-        const promptCheckCommand = 'npx kspec session prompt-check';
+        const promptCheckCommand = "kspec session prompt-check";
         const existingPromptHooks = hooks.UserPromptSubmit;
-        const promptAlreadyInstalled = existingPromptHooks?.some((entry) => entry.hooks?.some((hook) => hook.command?.includes('session prompt-check')));
+        const promptAlreadyInstalled = existingPromptHooks?.some((entry) => entry.hooks?.some((hook) => hook.command?.includes("session prompt-check")));
         if (!promptAlreadyInstalled) {
             hooks.UserPromptSubmit = [
                 ...(existingPromptHooks || []),
                 {
                     hooks: [
                         {
-                            type: 'command',
+                            type: "command",
                             command: promptCheckCommand,
                         },
                     ],
@@ -167,17 +407,17 @@ async function installClaudeCodeHooks(projectDir) {
             result.promptCheck = true; // Already configured
         }
         // Install Stop hook (checkpoint)
-        const stopHookCommand = 'npx kspec session checkpoint --json';
+        const stopHookCommand = "kspec session checkpoint --json";
         const existingStopHooks = hooks.Stop;
-        const stopAlreadyInstalled = existingStopHooks?.some((entry) => entry.hooks?.some((hook) => hook.command?.includes('session checkpoint')));
+        const stopAlreadyInstalled = existingStopHooks?.some((entry) => entry.hooks?.some((hook) => hook.command?.includes("session checkpoint")));
         if (!stopAlreadyInstalled) {
             hooks.Stop = [
                 ...(existingStopHooks || []),
                 {
-                    matcher: '',
+                    matcher: "",
                     hooks: [
                         {
-                            type: 'command',
+                            type: "command",
                             command: stopHookCommand,
                         },
                     ],
@@ -188,65 +428,46 @@ async function installClaudeCodeHooks(projectDir) {
         else {
             result.stop = true; // Already configured
         }
-        config.hooks = hooks;
-        // Write back
-        await fs.writeFile(configPath, JSON.stringify(config, null, 2) + '\n', 'utf-8');
-        return result;
-    }
-    catch {
-        return result;
-    }
-}
-/**
- * Install stop hook to project-level Claude Code settings (.claude/settings.json)
- * @deprecated Use installClaudeCodeHooks instead
- */
-async function installClaudeCodeStopHook(projectDir) {
-    const configPath = path.join(projectDir, '.claude', 'settings.json');
-    const configDir = path.dirname(configPath);
-    try {
-        // Ensure directory exists
-        await fs.mkdir(configDir, { recursive: true });
-        // Read existing config or start fresh
-        let config = {};
-        try {
-            const existing = await fs.readFile(configPath, 'utf-8');
-            config = JSON.parse(existing);
+        // AC: @enhanced-setup ac-2 - Install PreToolUse hooks with guards
+        const existingPreToolUseHooks = hooks.PreToolUse;
+        // Check if our guards are already installed
+        const guardHookCommands = Object.keys(GUARD_SCRIPTS).map((name) => `.claude/hooks/${name}`);
+        const guardsAlreadyInstalled = existingPreToolUseHooks?.some((entry) => entry.hooks?.some((hook) => guardHookCommands.some((cmd) => hook.command?.includes(cmd))));
+        if (!guardsAlreadyInstalled) {
+            // Create guard script files
+            for (const [name, content] of Object.entries(GUARD_SCRIPTS)) {
+                const scriptPath = path.join(hooksDir, name);
+                if (!dryRun) {
+                    await fs.writeFile(scriptPath, content, { mode: 0o755 });
+                }
+                result.guardsCreated.push(name);
+            }
+            // Add PreToolUse hook entry
+            hooks.PreToolUse = [
+                ...(existingPreToolUseHooks || []),
+                {
+                    matcher: "Bash",
+                    hooks: Object.keys(GUARD_SCRIPTS).map((name) => ({
+                        type: "command",
+                        command: `.claude/hooks/${name}`,
+                    })),
+                },
+            ];
+            result.preToolUse = true;
         }
-        catch {
-            // File doesn't exist or invalid JSON, start fresh
+        else {
+            result.preToolUse = true; // Already configured
         }
-        // Build the stop hook command
-        const stopHookCommand = 'npx kspec session checkpoint --json';
-        // Get or create hooks object
-        const hooks = config.hooks || {};
-        // Check if Stop hook already exists with our command
-        const existingStopHooks = hooks.Stop;
-        const alreadyInstalled = existingStopHooks?.some((entry) => entry.hooks?.some((hook) => hook.command?.includes('session checkpoint')));
-        if (alreadyInstalled) {
-            return true; // Already configured
-        }
-        // Add our stop hook using Claude Code hooks format
-        // Note: matcher field is required even if empty string
-        hooks.Stop = [
-            ...(existingStopHooks || []),
-            {
-                matcher: '',
-                hooks: [
-                    {
-                        type: 'command',
-                        command: stopHookCommand,
-                    },
-                ],
-            },
-        ];
         config.hooks = hooks;
         // Write back
-        await fs.writeFile(configPath, JSON.stringify(config, null, 2) + '\n', 'utf-8');
-        return true;
+        if (!dryRun) {
+            await fs.writeFile(configPath, `${JSON.stringify(config, null, 2)}\n`, "utf-8");
+        }
+        return result;
     }
-    catch {
-        return false;
+    catch (err) {
+        debugLog("installClaudeCodeHooks failed", err);
+        return result;
     }
 }
 /**
@@ -254,23 +475,23 @@ async function installClaudeCodeStopHook(projectDir) {
  * Aider uses `set-env:` for environment variables in list format
  */
 async function installAiderConfig(author) {
-    const configPath = path.join(os.homedir(), '.aider.conf.yml');
+    const configPath = path.join(os.homedir(), ".aider.conf.yml");
     try {
-        let content = '';
+        let content = "";
         try {
-            content = await fs.readFile(configPath, 'utf-8');
+            content = await fs.readFile(configPath, "utf-8");
         }
-        catch {
-            // File doesn't exist, start fresh
+        catch (err) {
+            debugLog("No existing Aider config, starting fresh", err);
         }
         // Check if KSPEC_AUTHOR is already set
-        if (content.includes('KSPEC_AUTHOR')) {
+        if (content.includes("KSPEC_AUTHOR")) {
             // Replace existing value (handles both old and new format)
             content = content.replace(/^(\s*-?\s*KSPEC_AUTHOR\s*[=:]\s*).*$/m, `  - KSPEC_AUTHOR=${author}`);
         }
         else {
             // Add to set-env section or create it
-            if (content.includes('set-env:')) {
+            if (content.includes("set-env:")) {
                 // Append to existing set-env section
                 content = content.replace(/(set-env:\s*\n)/m, `$1  - KSPEC_AUTHOR=${author}\n`);
             }
@@ -279,10 +500,11 @@ async function installAiderConfig(author) {
                 content += `\n# kspec author for note attribution\nset-env:\n  - KSPEC_AUTHOR=${author}\n`;
             }
         }
-        await fs.writeFile(configPath, content, 'utf-8');
+        await fs.writeFile(configPath, content, "utf-8");
         return true;
     }
-    catch {
+    catch (err) {
+        debugLog("installAiderConfig failed", err);
         return false;
     }
 }
@@ -295,19 +517,20 @@ async function installGenericJsonConfig(configPath, author) {
         await fs.mkdir(configDir, { recursive: true });
         let config = {};
         try {
-            const existing = await fs.readFile(configPath, 'utf-8');
+            const existing = await fs.readFile(configPath, "utf-8");
             config = JSON.parse(existing);
         }
-        catch {
-            // Start fresh
+        catch (err) {
+            debugLog(`No existing config at ${configPath}, starting fresh`, err);
         }
         const env = config.env || {};
         env.KSPEC_AUTHOR = author;
         config.env = env;
-        await fs.writeFile(configPath, JSON.stringify(config, null, 2) + '\n', 'utf-8');
+        await fs.writeFile(configPath, `${JSON.stringify(config, null, 2)}\n`, "utf-8");
         return true;
     }
-    catch {
+    catch (err) {
+        debugLog(`installGenericJsonConfig failed for ${configPath}`, err);
         return false;
     }
 }
@@ -316,26 +539,26 @@ async function installGenericJsonConfig(configPath, author) {
  */
 function getDefaultAuthor(agentType) {
     switch (agentType) {
-        case 'claude-code':
-            return '@claude';
-        case 'cline':
-            return '@cline';
-        case 'roo-code':
-            return '@roo';
-        case 'copilot-cli':
-            return '@copilot';
-        case 'gemini-cli':
-            return '@gemini';
-        case 'codex-cli':
-            return '@codex';
-        case 'aider':
-            return '@aider';
-        case 'opencode':
-            return '@opencode';
-        case 'amp':
-            return '@amp';
+        case "claude-code":
+            return "@claude";
+        case "cline":
+            return "@cline";
+        case "roo-code":
+            return "@roo";
+        case "copilot-cli":
+            return "@copilot";
+        case "gemini-cli":
+            return "@gemini";
+        case "codex-cli":
+            return "@codex";
+        case "aider":
+            return "@aider";
+        case "opencode":
+            return "@opencode";
+        case "amp":
+            return "@amp";
         default:
-            return '@agent';
+            return "@agent";
     }
 }
 /**
@@ -348,7 +571,7 @@ async function promptYesNo(question) {
     });
     try {
         const answer = await rl.question(`${question} `);
-        return answer.toLowerCase() === 'y';
+        return answer.toLowerCase() === "y";
     }
     finally {
         rl.close();
@@ -379,7 +602,7 @@ async function ensureWorktree(autoWorktree) {
             console.log(`Detected ${SHADOW_BRANCH_NAME} branch without .kspec worktree. Creating...`);
             const result = await repairShadow(projectRoot);
             if (result.success) {
-                success('Created .kspec worktree');
+                success("Created .kspec worktree");
                 return true;
             }
             else {
@@ -390,10 +613,10 @@ async function ensureWorktree(autoWorktree) {
         // AC: detect-existing-repo - prompt user
         const shouldCreate = await promptYesNo(`${SHADOW_BRANCH_NAME} branch exists but .kspec worktree is missing. Create it? (y/N)`);
         if (shouldCreate) {
-            console.log('Creating .kspec worktree...');
+            console.log("Creating .kspec worktree...");
             const result = await repairShadow(projectRoot);
             if (result.success) {
-                success('Created .kspec worktree');
+                success("Created .kspec worktree");
                 return true;
             }
             else {
@@ -402,7 +625,7 @@ async function ensureWorktree(autoWorktree) {
             }
         }
         else {
-            warn('Skipping worktree creation');
+            warn("Skipping worktree creation");
             return false;
         }
     }
@@ -414,76 +637,837 @@ async function ensureWorktree(autoWorktree) {
  */
 function printManualInstructions(agentType) {
     const author = getDefaultAuthor(agentType);
-    console.log('\nManual setup instructions:\n');
+    console.log("\nManual setup instructions:\n");
     switch (agentType) {
-        case 'claude-code':
-            console.log('Add to ~/.claude/settings.json:');
-            console.log('```json');
+        case "claude-code":
+            console.log("Add to ~/.claude/settings.json:");
+            console.log("```json");
             console.log(JSON.stringify({ env: { KSPEC_AUTHOR: author } }, null, 2));
-            console.log('```');
+            console.log("```");
             break;
-        case 'cline':
-        case 'roo-code':
-            console.log('Add to your shell profile (~/.bashrc, ~/.zshrc):');
-            console.log('```bash');
+        case "cline":
+        case "roo-code":
+            console.log("Add to your shell profile (~/.bashrc, ~/.zshrc):");
+            console.log("```bash");
             console.log(`export KSPEC_AUTHOR="${author}"`);
-            console.log('```');
-            console.log('\nThis will be inherited by terminals spawned by the VS Code extension.');
+            console.log("```");
+            console.log("\nThis will be inherited by terminals spawned by the VS Code extension.");
             break;
-        case 'copilot-cli':
-            console.log('Add to ~/.copilot/config.json:');
-            console.log('```json');
+        case "copilot-cli":
+            console.log("Add to ~/.copilot/config.json:");
+            console.log("```json");
             console.log(JSON.stringify({ env: { KSPEC_AUTHOR: author } }, null, 2));
-            console.log('```');
+            console.log("```");
             break;
-        case 'aider':
-            console.log('Add to ~/.aider.conf.yml:');
-            console.log('```yaml');
-            console.log('set-env:');
+        case "aider":
+            console.log("Add to ~/.aider.conf.yml:");
+            console.log("```yaml");
+            console.log("set-env:");
             console.log(`  - KSPEC_AUTHOR=${author}`);
-            console.log('```');
+            console.log("```");
             break;
-        case 'codex-cli':
-            console.log('Add to ~/.codex/config.toml:');
-            console.log('```toml');
-            console.log('[shell_environment_policy]');
+        case "codex-cli":
+            console.log("Add to ~/.codex/config.toml:");
+            console.log("```toml");
+            console.log("[shell_environment_policy]");
             console.log(`set = { KSPEC_AUTHOR = "${author}" }`);
-            console.log('```');
+            console.log("```");
             break;
-        case 'opencode':
-            console.log('Add to ~/.config/opencode/opencode.json:');
-            console.log('```json');
+        case "opencode":
+            console.log("Add to ~/.config/opencode/opencode.json:");
+            console.log("```json");
             console.log(JSON.stringify({ env: { KSPEC_AUTHOR: author } }, null, 2));
-            console.log('```');
+            console.log("```");
             break;
-        case 'amp':
-            console.log('Add to ~/.config/amp/settings.json:');
-            console.log('```json');
+        case "amp":
+            console.log("Add to ~/.config/amp/settings.json:");
+            console.log("```json");
             console.log(JSON.stringify({ env: { KSPEC_AUTHOR: author } }, null, 2));
-            console.log('```');
+            console.log("```");
             break;
         default:
-            console.log('Set the KSPEC_AUTHOR environment variable:');
-            console.log('```bash');
+            console.log("Set the KSPEC_AUTHOR environment variable:");
+            console.log("```bash");
             console.log(`export KSPEC_AUTHOR="${author}"`);
-            console.log('```');
-            console.log('\nOr add to your shell profile (~/.bashrc, ~/.zshrc, etc.)');
+            console.log("```");
+            console.log("\nOr add to your shell profile (~/.bashrc, ~/.zshrc, etc.)");
+    }
+}
+/**
+ * Check the current setup status
+ * AC: @enhanced-setup ac-7, ac-8
+ */
+async function getSetupStatus(projectDir) {
+    const detected = detectAgent();
+    const configPath = path.join(projectDir, ".claude", "settings.json");
+    const hooksDir = path.join(projectDir, ".claude", "hooks");
+    const agentsMdPath = path.join(projectDir, "kspec-agents.md");
+    const hashPath = path.join(projectDir, ".kspec", ".kspec-agents-hash");
+    const skillsDir = path.join(projectDir, ".claude", "skills");
+    // Check hooks
+    const hooks = {
+        promptCheck: false,
+        stop: false,
+        preToolUse: false,
+        guardsPresent: [],
+    };
+    try {
+        const configContent = await fs.readFile(configPath, "utf-8");
+        const config = JSON.parse(configContent);
+        const hooksConfig = config.hooks || {};
+        // Check UserPromptSubmit
+        const promptHooks = hooksConfig.UserPromptSubmit;
+        hooks.promptCheck = promptHooks?.some((entry) => entry.hooks?.some((h) => h.command?.includes("prompt-check"))) ?? false;
+        // Check Stop
+        const stopHooks = hooksConfig.Stop;
+        hooks.stop = stopHooks?.some((entry) => entry.hooks?.some((h) => h.command?.includes("checkpoint"))) ?? false;
+        // Check PreToolUse
+        const preToolUseHooks = hooksConfig.PreToolUse;
+        hooks.preToolUse = preToolUseHooks?.some((entry) => entry.hooks?.some((h) => h.command?.includes(".claude/hooks/"))) ?? false;
+    }
+    catch (err) {
+        debugLog("Failed to read hooks config for status", err);
+    }
+    // Check guard scripts
+    try {
+        const guardFiles = await fs.readdir(hooksDir);
+        for (const name of Object.keys(GUARD_SCRIPTS)) {
+            if (guardFiles.includes(name)) {
+                hooks.guardsPresent.push(name);
+            }
+        }
+    }
+    catch (err) {
+        debugLog("Hooks dir doesn't exist", err);
+    }
+    // Check skills
+    const skills = {
+        total: 0,
+        rendered: 0,
+        drifted: 0,
+    };
+    // Helper to scan a directory for skill subdirs with kspec-managed SKILL.md
+    async function scanForSkills(baseDir) {
+        try {
+            const dirs = await fs.readdir(baseDir, { withFileTypes: true });
+            for (const dir of dirs) {
+                if (dir.isDirectory()) {
+                    const skillMdPath = path.join(baseDir, dir.name, "SKILL.md");
+                    try {
+                        const content = await fs.readFile(skillMdPath, "utf-8");
+                        if (content.includes("<!-- kspec-managed -->")) {
+                            skills.total++;
+                            skills.rendered++;
+                        }
+                    }
+                    catch (_noSkillMd) {
+                        // No SKILL.md
+                    }
+                }
+            }
+        }
+        catch (_notReadable) {
+            // Directory doesn't exist
+        }
+    }
+    // Scan .claude/skills/ (project/local skills)
+    await scanForSkills(skillsDir);
+    // Check plugin marketplace health
+    // AC: @enhanced-setup ac-7, ac-8
+    const plugin = {
+        marketplaceRegistered: false,
+        marketplaceHealthy: false,
+        pluginEnabled: false,
+    };
+    try {
+        const { checkMarketplaceHealth } = await import("../../lib/claude-plugin-registry.js");
+        const health = await checkMarketplaceHealth();
+        plugin.marketplaceRegistered = health.status !== "missing";
+        plugin.marketplaceHealthy = health.status === "healthy";
+        plugin.registeredPath = health.registeredPath;
+        plugin.healthMessage = health.message;
+    }
+    catch (err) {
+        debugLog("Could not check marketplace health", err);
+        plugin.healthMessage = "Health check unavailable";
+    }
+    // Check if plugin is enabled in project settings
+    try {
+        const configContent = await fs.readFile(configPath, "utf-8");
+        const config = JSON.parse(configContent);
+        plugin.pluginEnabled = config.enabledPlugins?.["kspec@kspec-plugins"] === true;
+    }
+    catch (err) {
+        debugLog("Could not check plugin enablement", err);
+    }
+    // Check agents.md
+    const agentsMd = {
+        exists: false,
+        status: "missing",
+    };
+    try {
+        await fs.access(agentsMdPath);
+        agentsMd.exists = true;
+        try {
+            const hashContent = await fs.readFile(hashPath, "utf-8");
+            const hashData = JSON.parse(hashContent);
+            agentsMd.generatedAt = hashData.generatedAt;
+            // AC: @cross-platform-and-version-robustness ac-4
+            // Compare stored hash against current meta to detect staleness
+            try {
+                const { initContext, loadMetaContext } = await import("../../parser/index.js");
+                const { computeMetaHash, loadTemplateSections, getPackageRoot } = await import("./agents.js");
+                const ctx = await initContext();
+                if (ctx.manifestPath) {
+                    const metaCtx = await loadMetaContext(ctx);
+                    let templateSections = [];
+                    try {
+                        templateSections = await loadTemplateSections(getPackageRoot());
+                    }
+                    catch (err) {
+                        debugLog("Templates not available for staleness check", err);
+                    }
+                    const currentHash = computeMetaHash(metaCtx.skills, metaCtx.conventions, metaCtx.workflows, templateSections);
+                    agentsMd.status = hashData.metaHash === currentHash ? "current" : "stale";
+                }
+                else {
+                    // AC: @doctor-command ac-staleness-unknown — no manifest means we can't determine staleness
+                    agentsMd.status = "unknown";
+                }
+            }
+            catch (err) {
+                // AC: @doctor-command ac-staleness-unknown — hash computation failed
+                debugLog("Could not compute meta hash for staleness check", err);
+                agentsMd.status = "unknown";
+            }
+        }
+        catch (err) {
+            debugLog("Hash file missing or invalid, marking stale", err);
+            agentsMd.status = "stale";
+        }
+    }
+    catch (err) {
+        debugLog("kspec-agents.md doesn't exist", err);
+    }
+    // Check seeding state
+    const seeding = {
+        permissionsSeeded: false,
+        memorySeeded: false,
+    };
+    try {
+        const configContent = await fs.readFile(path.join(projectDir, ".claude", "settings.json"), "utf-8");
+        const config = JSON.parse(configContent);
+        seeding.permissionsSeeded = !!config.permissions;
+    }
+    catch (err) {
+        debugLog("Could not check permissions seeding state", err);
+    }
+    if (detected.type === "claude-code") {
+        try {
+            const { claudeCodeMemoryWriter } = await import("./setup-seeding.js");
+            const memoryExists = await claudeCodeMemoryWriter.exists(projectDir);
+            seeding.memorySeeded = memoryExists;
+            if (memoryExists) {
+                seeding.memoryPath = claudeCodeMemoryWriter.getMemoryPath(projectDir);
+            }
+        }
+        catch (err) {
+            debugLog("Could not check memory seeding state", err);
+        }
+    }
+    return {
+        agent: {
+            detected: detected.type,
+            confidence: detected.confidence,
+        },
+        hooks,
+        skills,
+        plugin,
+        agentsMd,
+        seeding,
+    };
+}
+/**
+ * Render skills using the platform renderer registry
+ * AC: @setup-pipeline-unification ac-2 - uses getRenderer/getAllRenderers, not legacy renderClaudeCodeSkill
+ * AC: @setup-pipeline-unification ac-4 - errors logged at debug level
+ */
+async function renderSkillsForSetup(projectDir, dryRun) {
+    // Dynamically import to avoid circular dependencies
+    const { initContext, loadMetaContext } = await import("../../parser/index.js");
+    const { getRenderer } = await import("../../parser/skill-render.js");
+    try {
+        const ctx = await initContext();
+        if (!ctx.manifestPath) {
+            return { rendered: 0, skipped: 0, pluginProvided: 0, skillIds: [] };
+        }
+        const metaCtx = await loadMetaContext(ctx);
+        // Collect all skills that have a registered renderer for their platform
+        const skillsToRender = [];
+        for (const skill of metaCtx.skills) {
+            for (const platform of skill.platforms) {
+                const renderer = getRenderer(platform);
+                if (renderer) {
+                    skillsToRender.push({ skill, platform });
+                }
+            }
+        }
+        if (skillsToRender.length === 0) {
+            return { rendered: 0, skipped: 0, pluginProvided: 0, skillIds: [] };
+        }
+        let rendered = 0;
+        let skipped = 0;
+        let pluginProvided = 0;
+        const skillIds = [];
+        for (const { skill, platform } of skillsToRender) {
+            const renderer = getRenderer(platform);
+            try {
+                const result = await renderer.render(ctx, projectDir, skill, {
+                    dryRun,
+                });
+                if (result.action === "created" || result.action === "updated") {
+                    rendered++;
+                    if (!skillIds.includes(skill.id)) {
+                        skillIds.push(skill.id);
+                    }
+                }
+                else if (result.action === "skipped" && result.skipCode === "plugin-provided") {
+                    pluginProvided++;
+                }
+                else {
+                    skipped++;
+                }
+            }
+            catch (err) {
+                debugLog(`Failed to render skill ${skill.id} for ${platform}`, err);
+                skipped++;
+            }
+        }
+        return { rendered, skipped, pluginProvided, skillIds };
+    }
+    catch (err) {
+        debugLog("renderSkillsForSetup failed", err);
+        return { rendered: 0, skipped: 0, pluginProvided: 0, skillIds: [] };
+    }
+}
+/**
+ * Generate kspec-agents.md using the canonical implementation from agents.ts
+ * AC: @setup-pipeline-unification ac-1 - calls generateAgentsContent() from agents.ts
+ * AC: @setup-pipeline-unification ac-4 - errors logged at debug level
+ */
+async function generateAgentInstructions(projectDir, dryRun) {
+    const outputPath = path.join(projectDir, "kspec-agents.md");
+    const hashPath = path.join(projectDir, ".kspec", ".kspec-agents-hash");
+    // Dynamically import to avoid circular dependencies
+    const { initContext, loadMetaContext } = await import("../../parser/index.js");
+    const { generateAgentsContent, loadTemplateSections, getPackageRoot, computeMetaHash, } = await import("./agents.js");
+    try {
+        const ctx = await initContext();
+        if (!ctx.manifestPath) {
+            return { success: false, path: outputPath };
+        }
+        const metaCtx = await loadMetaContext(ctx);
+        const timestamp = new Date().toISOString();
+        // Load templates using the canonical implementation
+        let templateSections = [];
+        try {
+            templateSections = await loadTemplateSections(getPackageRoot());
+        }
+        catch (err) {
+            debugLog("Failed to load template sections", err);
+        }
+        // Generate content using the canonical implementation from agents.ts
+        const content = await generateAgentsContent(metaCtx.skills, metaCtx.conventions, metaCtx.workflows, timestamp, templateSections);
+        if (!dryRun) {
+            await fs.writeFile(outputPath, content, "utf-8");
+            // Write hash for freshness tracking using the canonical hash function
+            const metaHash = computeMetaHash(metaCtx.skills, metaCtx.conventions, metaCtx.workflows, templateSections);
+            await fs.mkdir(path.dirname(hashPath), { recursive: true });
+            // Dynamically import version to avoid top-level require
+            const { createRequire } = await import("node:module");
+            const req = createRequire(import.meta.url);
+            const { version } = req("../../../package.json");
+            await fs.writeFile(hashPath, JSON.stringify({
+                metaHash,
+                generatedAt: timestamp,
+                version,
+            }, null, 2), "utf-8");
+        }
+        return { success: true, path: outputPath };
+    }
+    catch (err) {
+        debugLog("generateAgentInstructions failed", err);
+        return { success: false, path: outputPath };
+    }
+}
+/**
+ * Install core skills for the setup pipeline
+ * AC: @init-setup-integration ac-2 - core skills installed
+ */
+async function installCoreSkillsForSetup(projectDir, dryRun) {
+    // Dynamically import to avoid circular dependencies
+    const { initContext, loadMetaContext, saveMetaItem, getSkillContentPath, } = await import("../../parser/index.js");
+    const { commitIfShadow } = await import("../../parser/shadow.js");
+    const { SkillSchema } = await import("../../schema/index.js");
+    const { loadCoreSkillsManifest, copyCoreSkillFiles, getKspecPackageVersion, } = await import("./skill.js");
+    const { ulid } = await import("ulid");
+    let installed = 0;
+    let skipped = 0;
+    try {
+        const ctx = await initContext();
+        if (!ctx.manifestPath) {
+            return { installed: 0, skipped: 0 };
+        }
+        const metaCtx = await loadMetaContext(ctx);
+        const coreSkills = await loadCoreSkillsManifest();
+        // AC: @cross-platform-and-version-robustness ac-3
+        const kspecVersion = await getKspecPackageVersion();
+        if (!kspecVersion) {
+            debugLog("Could not determine kspec version — skills installed without version tracking");
+        }
+        for (const coreSkill of coreSkills) {
+            // Check if skill exists
+            const existingSkill = metaCtx.skills.find((s) => s.id === coreSkill.id);
+            if (existingSkill && existingSkill.origin !== "core") {
+                // Custom/project skill exists, skip
+                skipped++;
+                continue;
+            }
+            // Build skill data
+            const skillData = {
+                _ulid: existingSkill?._ulid || ulid(),
+                id: coreSkill.id,
+                name: coreSkill.name,
+                description: coreSkill.description,
+                origin: "core",
+                ...(kspecVersion && { version: kspecVersion }),
+                platforms: coreSkill.platforms || ["claude-code"],
+                depends_on: [],
+                tags: ["core"],
+            };
+            const parsed = SkillSchema.safeParse(skillData);
+            if (!parsed.success) {
+                skipped++;
+                continue;
+            }
+            if (!dryRun) {
+                await saveMetaItem(ctx, parsed.data, "skill");
+                // Copy skill files (SKILL.md + supporting dirs)
+                const targetDir = path.dirname(getSkillContentPath(ctx, parsed.data.id));
+                await copyCoreSkillFiles(coreSkill.id, targetDir);
+            }
+            installed++;
+        }
+        // Commit changes
+        if (!dryRun && installed > 0) {
+            const ctx2 = await initContext();
+            await commitIfShadow(ctx2.shadow, "skill-install-core", `${installed} core skills`);
+        }
+        // AC: @core-skill-install ac-6, ac-7 - Register marketplace and enable plugin
+        let marketplaceResult;
+        let enableResult;
+        if (!dryRun) {
+            const { registerCorePluginMarketplace, enablePluginInProject, } = await import("../../lib/claude-plugin-registry.js");
+            marketplaceResult = await registerCorePluginMarketplace();
+            enableResult = await enablePluginInProject(projectDir);
+        }
+        return {
+            installed,
+            skipped,
+            marketplaceRegistered: marketplaceResult?.success ?? false,
+            pluginEnabled: enableResult?.success ?? false,
+            marketplaceMessage: marketplaceResult?.message,
+            enableMessage: enableResult?.message,
+        };
+    }
+    catch (err) {
+        debugLog("installCoreSkillsForSetup failed", err);
+        return { installed: 0, skipped: 0 };
+    }
+}
+/**
+ * Run the full setup pipeline programmatically.
+ * Used by both 'kspec setup' command and 'kspec init --setup'.
+ * AC: @init-setup-integration ac-2, ac-3
+ */
+export async function runSetupPipeline(projectDir, options) {
+    const dryRun = options.dryRun ?? false;
+    const skipSkills = options.skipSkills ?? false;
+    const installHooksFlag = options.installHooks ?? true;
+    const steps = [];
+    let coreSkillsInstalled = 0;
+    let skillsRendered = 0;
+    let hooksInstalled = false;
+    let agentsMdGenerated = false;
+    let permissionsSeeded = false;
+    let memorySeeded = false;
+    try {
+        const detected = detectAgent();
+        // Step 1: Agent detection
+        steps.push({
+            name: "Agent detection",
+            status: "done",
+            message: `${detected.type} (${detected.confidence} confidence)`,
+        });
+        // Step 2: Install core skills
+        // AC: @init-setup-integration ac-2 - core skills installed in .kspec/skills/
+        const coreResult = await installCoreSkillsForSetup(projectDir, dryRun);
+        coreSkillsInstalled = coreResult.installed;
+        if (coreResult.installed > 0 || coreResult.skipped > 0) {
+            steps.push({
+                name: "Install core skills",
+                status: "done",
+                message: `${coreResult.installed} installed, ${coreResult.skipped} skipped`,
+            });
+        }
+        else {
+            steps.push({
+                name: "Install core skills",
+                status: "skipped",
+                message: "No core skills found in package",
+            });
+        }
+        // Step 2b: Register plugin marketplace (reports result from installCoreSkillsForSetup)
+        // AC: @core-skill-install ac-6, ac-7
+        if (!dryRun && (coreResult.installed > 0 || coreResult.skipped > 0)) {
+            const bothOk = coreResult.marketplaceRegistered && coreResult.pluginEnabled;
+            if (bothOk) {
+                steps.push({
+                    name: "Register plugin marketplace",
+                    status: "done",
+                    message: "marketplace registered, plugin enabled",
+                });
+            }
+            else {
+                const failures = [];
+                if (!coreResult.marketplaceRegistered) {
+                    failures.push(coreResult.marketplaceMessage || "marketplace registration failed");
+                }
+                if (!coreResult.pluginEnabled) {
+                    failures.push(coreResult.enableMessage || "plugin enablement failed");
+                }
+                steps.push({
+                    name: "Register plugin marketplace",
+                    status: "failed",
+                    message: failures.join("; "),
+                });
+            }
+        }
+        // Step 3: Install hooks (Claude Code only)
+        // AC: @init-setup-integration ac-3 - hooks present
+        if (detected.type === "claude-code" && installHooksFlag) {
+            const hooksResult = await installClaudeCodeHooks(projectDir, dryRun);
+            const installedHooks = [];
+            if (hooksResult.promptCheck)
+                installedHooks.push("UserPromptSubmit");
+            if (hooksResult.stop)
+                installedHooks.push("Stop");
+            if (hooksResult.preToolUse)
+                installedHooks.push("PreToolUse");
+            hooksInstalled =
+                hooksResult.promptCheck || hooksResult.stop || hooksResult.preToolUse;
+            steps.push({
+                name: "Install hooks",
+                status: "done",
+                message: installedHooks.join(", "),
+                details: {
+                    guards: hooksResult.guardsCreated,
+                },
+            });
+        }
+        else if (!installHooksFlag) {
+            steps.push({
+                name: "Install hooks",
+                status: "skipped",
+                message: "--no-hooks flag",
+            });
+        }
+        else {
+            steps.push({
+                name: "Install hooks",
+                status: "skipped",
+                message: `not applicable for ${detected.type}`,
+            });
+        }
+        // Step 3a: Ensure artifacts directory exists
+        // AC: @artifacts-directory ac-setup-ensures
+        {
+            const artifactsDir = path.join(projectDir, ".kspec", "artifacts");
+            let artifactsCreated = false;
+            try {
+                await fs.access(artifactsDir);
+            }
+            catch (_e) {
+                if (!dryRun) {
+                    await fs.mkdir(artifactsDir, { recursive: true });
+                }
+                artifactsCreated = true;
+            }
+            steps.push({
+                name: "Ensure artifacts directory",
+                status: artifactsCreated ? "done" : "skipped",
+                message: artifactsCreated ? "created .kspec/artifacts/" : "already exists",
+            });
+        }
+        // Step 3b: Seed permissions (Claude Code only)
+        // AC: @new-project-bootstrapping ac-1
+        {
+            const { seedPermissions } = await import("./setup-seeding.js");
+            const permResult = await seedPermissions(projectDir, detected.type, {
+                dryRun,
+                force: options.force,
+            });
+            permissionsSeeded = permResult.seeded;
+            steps.push({
+                name: "Seed permissions",
+                status: permResult.seeded ? "done" : "skipped",
+                message: permResult.message,
+            });
+        }
+        // Step 3c: Seed memory (platform-extensible)
+        // AC: @new-project-bootstrapping ac-2
+        {
+            const { seedMemory } = await import("./setup-seeding.js");
+            const memResult = await seedMemory(projectDir, detected.type, {
+                dryRun,
+                force: options.force,
+            });
+            memorySeeded = memResult.seeded;
+            steps.push({
+                name: "Seed memory",
+                status: memResult.seeded ? "done" : "skipped",
+                message: memResult.seeded ? memResult.path : memResult.message,
+            });
+        }
+        // Step 4: Render skills
+        // AC: @init-setup-integration ac-3 - rendered skill files present
+        if (!skipSkills) {
+            const skillsResult = await renderSkillsForSetup(projectDir, dryRun);
+            skillsRendered = skillsResult.rendered;
+            if (skillsResult.rendered > 0 || skillsResult.skipped > 0 || skillsResult.pluginProvided > 0) {
+                const parts = [];
+                if (skillsResult.rendered > 0)
+                    parts.push(`${skillsResult.rendered} rendered`);
+                if (skillsResult.pluginProvided > 0)
+                    parts.push(`${skillsResult.pluginProvided} plugin-provided`);
+                if (skillsResult.skipped > 0)
+                    parts.push(`${skillsResult.skipped} unchanged`);
+                steps.push({
+                    name: "Render skills",
+                    status: "done",
+                    message: parts.join(", "),
+                    details: {
+                        skillIds: skillsResult.skillIds,
+                    },
+                });
+            }
+            else {
+                steps.push({
+                    name: "Render skills",
+                    status: "skipped",
+                    message: "No claude-code skills in meta",
+                });
+            }
+        }
+        else {
+            steps.push({
+                name: "Render skills",
+                status: "skipped",
+                message: "--skip-skills flag",
+            });
+        }
+        // Step 5: Generate kspec-agents.md
+        // AC: @init-setup-integration ac-3 - kspec-agents.md present
+        const agentsResult = await generateAgentInstructions(projectDir, dryRun);
+        agentsMdGenerated = agentsResult.success;
+        if (agentsResult.success) {
+            steps.push({
+                name: "Generate kspec-agents.md",
+                status: "done",
+                message: agentsResult.path,
+            });
+        }
+        else {
+            steps.push({
+                name: "Generate kspec-agents.md",
+                status: "failed",
+                message: "No kspec project found",
+            });
+        }
+        // Step 6: Configure author (optional, used by setup command)
+        if (options.configureAuthor) {
+            const author = options.author || getDefaultAuthor(detected.type);
+            if (!options.force && process.env.KSPEC_AUTHOR) {
+                steps.push({
+                    name: "Configure author",
+                    status: "skipped",
+                    message: `KSPEC_AUTHOR already set to "${process.env.KSPEC_AUTHOR}"`,
+                });
+            }
+            else {
+                let authorInstalled = false;
+                switch (detected.type) {
+                    case "claude-code":
+                        if (!dryRun) {
+                            authorInstalled = await installClaudeCodeConfig(author);
+                        }
+                        else {
+                            authorInstalled = true;
+                        }
+                        break;
+                    case "aider":
+                        if (!dryRun) {
+                            authorInstalled = await installAiderConfig(author);
+                        }
+                        else {
+                            authorInstalled = true;
+                        }
+                        break;
+                    default:
+                        break;
+                }
+                if (authorInstalled) {
+                    steps.push({
+                        name: "Configure author",
+                        status: "done",
+                        message: `KSPEC_AUTHOR="${author}"`,
+                    });
+                }
+            }
+        }
+        // Output summary
+        if (!dryRun) {
+            console.log(chalk.bold("kspec Setup Summary\n"));
+            for (const step of steps) {
+                const icon = step.status === "done"
+                    ? chalk.green("✓")
+                    : step.status === "skipped"
+                        ? chalk.gray("○")
+                        : chalk.red("✗");
+                const statusText = step.status === "done"
+                    ? ""
+                    : step.status === "skipped"
+                        ? chalk.gray(" (skipped)")
+                        : chalk.red(" (failed)");
+                console.log(`${icon} ${step.name}${statusText}`);
+                if (step.message) {
+                    console.log(chalk.gray(`  ${step.message}`));
+                }
+            }
+        }
+        const success = steps.every((s) => s.status !== "failed");
+        return {
+            success,
+            steps,
+            coreSkillsInstalled,
+            skillsRendered,
+            hooksInstalled,
+            agentsMdGenerated,
+            permissionsSeeded,
+            memorySeeded,
+        };
+    }
+    catch (err) {
+        debugLog("runSetupPipeline failed", err);
+        return {
+            success: false,
+            steps,
+            coreSkillsInstalled,
+            skillsRendered,
+            hooksInstalled,
+            agentsMdGenerated,
+            permissionsSeeded,
+            memorySeeded,
+        };
     }
 }
 /**
  * Register the 'setup' command
+ * AC: @enhanced-setup ac-1 through ac-9
  */
 export function registerSetupCommand(program) {
     program
-        .command('setup')
-        .description('Configure agent environment for kspec')
-        .option('--dry-run', 'Show what would be done without making changes')
-        .option('--author <author>', 'Custom author string (default: auto-detected based on agent)')
-        .option('--no-hooks', 'Skip installing Claude Code stop hook')
-        .option('--force', 'Overwrite existing configuration')
-        .option('--auto-worktree', 'Automatically create .kspec worktree if kspec-meta branch exists')
+        .command("setup")
+        .description("Configure agent environment for kspec (orchestrated pipeline)")
+        .option("--dry-run", "Show what would be done without making changes")
+        .option("--author <author>", "Custom author string (default: auto-detected based on agent)")
+        .option("--no-hooks", "Skip installing hooks")
+        .option("--skip-skills", "Skip rendering skills")
+        .option("--status", "Report current setup state without making changes")
+        .option("--force", "Overwrite existing configuration")
+        .option("--auto-worktree", "Automatically create .kspec worktree if kspec-meta branch exists")
         .action(async (options) => {
         try {
+            const projectDir = process.cwd();
+            // AC: @enhanced-setup ac-7, ac-8 - --status mode
+            if (options.status) {
+                const status = await getSetupStatus(projectDir);
+                output(status, () => {
+                    console.log(chalk.bold("kspec Setup Status\n"));
+                    // Agent detection
+                    console.log(chalk.gray("Agent:"));
+                    console.log(`  Detected: ${status.agent.detected} (${status.agent.confidence} confidence)`);
+                    console.log();
+                    // Hooks status
+                    console.log(chalk.gray("Hooks:"));
+                    console.log(`  UserPromptSubmit: ${status.hooks.promptCheck ? chalk.green("✓") : chalk.red("✗")}`);
+                    console.log(`  Stop:             ${status.hooks.stop ? chalk.green("✓") : chalk.red("✗")}`);
+                    console.log(`  PreToolUse:       ${status.hooks.preToolUse ? chalk.green("✓") : chalk.red("✗")}`);
+                    if (status.hooks.guardsPresent.length > 0) {
+                        console.log(`  Guards:           ${status.hooks.guardsPresent.join(", ")}`);
+                    }
+                    console.log();
+                    // Skills status
+                    console.log(chalk.gray("Skills:"));
+                    console.log(`  Rendered: ${status.skills.rendered}`);
+                    if (status.skills.drifted > 0) {
+                        console.log(`  Drifted:  ${chalk.yellow(status.skills.drifted.toString())}`);
+                    }
+                    console.log();
+                    // Plugin marketplace status
+                    // AC: @enhanced-setup ac-7, ac-8
+                    console.log(chalk.gray("Plugin:"));
+                    console.log(`  Marketplace: ${status.plugin.marketplaceRegistered ? (status.plugin.marketplaceHealthy ? chalk.green("healthy") : chalk.yellow("registered")) : chalk.red("not registered")}`);
+                    console.log(`  Enabled:     ${status.plugin.pluginEnabled ? chalk.green("✓") : chalk.red("✗")}`);
+                    if (status.plugin.registeredPath) {
+                        console.log(chalk.gray(`  Path: ${status.plugin.registeredPath}`));
+                    }
+                    if (status.plugin.healthMessage && !status.plugin.marketplaceHealthy) {
+                        console.log(chalk.yellow(`  ${status.plugin.healthMessage}`));
+                    }
+                    console.log();
+                    // Agents.md status
+                    console.log(chalk.gray("kspec-agents.md:"));
+                    if (status.agentsMd.exists) {
+                        // AC: @doctor-command ac-staleness-unknown — show appropriate color for unknown status
+                        const statusColor = status.agentsMd.status === "current"
+                            ? chalk.green
+                            : status.agentsMd.status === "unknown"
+                                ? chalk.yellow
+                                : chalk.yellow;
+                        console.log(`  Status: ${statusColor(status.agentsMd.status)}`);
+                        if (status.agentsMd.status === "unknown") {
+                            console.log(chalk.gray("  Could not determine staleness (no manifest or hash unavailable)"));
+                        }
+                        if (status.agentsMd.generatedAt) {
+                            console.log(`  Generated: ${status.agentsMd.generatedAt}`);
+                        }
+                    }
+                    else {
+                        console.log(`  Status: ${chalk.red("missing")}`);
+                        console.log(chalk.gray("  Run 'kspec setup' to generate"));
+                    }
+                    console.log();
+                    // Seeding status
+                    console.log(chalk.gray("Seeding:"));
+                    console.log(`  Permissions: ${status.seeding.permissionsSeeded ? chalk.green("✓") : chalk.gray("○")}`);
+                    console.log(`  Memory:      ${status.seeding.memorySeeded ? chalk.green("✓") : chalk.gray("○")}`);
+                    if (status.seeding.memoryPath) {
+                        console.log(chalk.gray(`  Path: ${status.seeding.memoryPath}`));
+                    }
+                });
+                return;
+            }
             // AC: detect-existing-repo, auto-worktree-flag, worktree-already-exists
             const worktreeReady = await ensureWorktree(options.autoWorktree || false);
             if (!worktreeReady) {
@@ -491,91 +1475,66 @@ export function registerSetupCommand(program) {
                 process.exit(EXIT_CODES.ERROR);
             }
             const detected = detectAgent();
-            const projectDir = process.cwd();
-            console.log(`Detected agent: ${detected.type} (confidence: ${detected.confidence})`);
-            if (detected.type === 'unknown') {
-                warn('Could not auto-detect agent environment');
-                printManualInstructions('unknown');
+            const dryRun = options.dryRun || false;
+            if (detected.type === "unknown") {
+                warn("Could not auto-detect agent environment");
+                printManualInstructions("unknown");
                 return;
             }
-            const author = options.author || getDefaultAuthor(detected.type);
-            const installHooks = options.hooks !== false && detected.type === 'claude-code';
-            if (options.dryRun) {
-                console.log(`\nWould configure:`);
-                console.log(`  Agent: ${detected.type}`);
-                console.log(`  Author: ${author}`);
-                if (detected.configPath) {
-                    console.log(`  Global config: ${detected.configPath}`);
-                }
-                if (installHooks) {
-                    console.log(`  Project config: ${path.join(projectDir, '.claude', 'settings.json')}`);
-                    console.log(`  Hooks: UserPromptSubmit (prompt-check), Stop (checkpoint)`);
+            // AC: @setup-pipeline-unification ac-3 - delegate to runSetupPipeline()
+            // One code path for both 'kspec setup' and 'kspec init --setup'
+            const result = await runSetupPipeline(projectDir, {
+                dryRun,
+                skipSkills: options.skipSkills || false,
+                installHooks: options.hooks !== false,
+                force: options.force || false,
+                author: options.author,
+                configureAuthor: true,
+            });
+            // AC: @enhanced-setup ac-1 - Display summary
+            // AC: @enhanced-setup ac-6 - dry-run displays planned actions
+            output({
+                dry_run: dryRun,
+                steps: result.steps.map((s) => ({
+                    name: s.name,
+                    status: s.status,
+                    message: s.message,
+                    details: s.details,
+                })),
+            }, () => {
+                if (dryRun) {
+                    console.log(chalk.yellow("DRY RUN - No changes made\n"));
                 }
-                return;
-            }
-            // Check if already configured
-            if (!options.force && process.env.KSPEC_AUTHOR) {
-                warn(`KSPEC_AUTHOR is already set to "${process.env.KSPEC_AUTHOR}"`);
-                console.log('Use --force to overwrite');
-                return;
-            }
-            // Install config based on agent type
-            let installed = false;
-            let hooksInstalled = false;
-            let hooksResult = null;
-            switch (detected.type) {
-                case 'claude-code':
-                    installed = await installClaudeCodeConfig(author);
-                    if (installHooks) {
-                        hooksResult = await installClaudeCodeHooks(projectDir);
-                        hooksInstalled = hooksResult.stop || hooksResult.promptCheck;
-                    }
-                    break;
-                case 'aider':
-                    installed = await installAiderConfig(author);
-                    break;
-                case 'cline':
-                case 'roo-code':
-                    // These VS Code extensions use shell env vars, not config files
-                    // Can't auto-install, must print instructions
-                    printManualInstructions(detected.type);
-                    return;
-                case 'copilot-cli':
-                case 'gemini-cli':
-                case 'opencode':
-                case 'amp':
-                    if (detected.configPath) {
-                        installed = await installGenericJsonConfig(detected.configPath, author);
+                // Pipeline already prints the summary when not dry-run
+                // For dry-run, print it here since the pipeline skips output
+                if (dryRun) {
+                    console.log(chalk.bold("kspec Setup Summary\n"));
+                    for (const step of result.steps) {
+                        const icon = step.status === "done"
+                            ? chalk.green("✓")
+                            : step.status === "skipped"
+                                ? chalk.gray("○")
+                                : chalk.red("✗");
+                        const statusText = step.status === "done"
+                            ? ""
+                            : step.status === "skipped"
+                                ? chalk.gray(" (skipped)")
+                                : chalk.red(" (failed)");
+                        console.log(`${icon} ${step.name}${statusText}`);
+                        if (step.message) {
+                            console.log(chalk.gray(`  ${step.message}`));
+                        }
                     }
-                    break;
-                case 'codex-cli':
-                    // Codex uses TOML config, would need special handling
-                    // For now, print manual instructions
-                    printManualInstructions(detected.type);
-                    return;
-            }
-            if (installed) {
-                success(`Configured ${detected.type} with KSPEC_AUTHOR="${author}"`, {
-                    agent: detected.type,
-                    author,
-                    configPath: detected.configPath,
-                });
-                if (hooksInstalled && hooksResult) {
-                    const installedHooks = [];
-                    if (hooksResult.promptCheck)
-                        installedHooks.push('UserPromptSubmit (prompt-check)');
-                    if (hooksResult.stop)
-                        installedHooks.push('Stop (checkpoint)');
-                    success(`Installed hooks to .claude/settings.json`, {
-                        hooks: installedHooks,
-                    });
                 }
-                console.log('\nRestart your agent session for changes to take effect.');
-            }
-            else {
-                error(errors.failures.installConfig(detected.type));
-                printManualInstructions(detected.type);
-            }
+                console.log();
+                if (dryRun) {
+                    console.log(chalk.yellow("Run without --dry-run to apply changes."));
+                }
+                else {
+                    console.log(chalk.green("Setup complete."));
+                    console.log(chalk.gray("Restart your agent session for changes to take effect."));
+                }
+            });
         }
         catch (err) {
             error(errors.failures.setupFailed, err);