Fix import paths and remove organ metaphors

- Update all `from storage.` imports to `from dss.storage.`
- Update `from config import config` to use `dss.settings`
- Update `from auth.` imports to `from dss.auth.`
- Update health check to use `dss.mcp.handler`
- Fix SmartMerger import (merger.py not smart_merger.py)
- Fix TranslationDictionary import path
- Fix test assertion for networkx edges/links
- Remove organ/body metaphors from:
  - API server health check
  - CLI status command and help text
  - Admin UI logger and error handler

🤖 Generated with [Claude Code](https://claude.com/claude-code)

Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>

apps/api/server.py

@@ -353,7 +353,7 @@ class TokenDriftCreate(BaseModel):
 
 # === Authentication ===
 
-from auth.atlassian_auth import get_auth
+from dss.auth.atlassian_auth import get_auth
 
 async def get_current_user(authorization: Optional[str] = Header(None)) -> Dict[str, Any]:
     """
@@ -421,71 +421,62 @@ async def root():
 @app.get("/health")
 async def health():
     """
-    🏥 ORGANISM VITAL SIGNS CHECK
+    Health check endpoint.
 
-    Performs a complete health diagnostic on the DSS component.
-    Returns 200 OK with vital signs if component is healthy.
+    Performs a complete health diagnostic on the DSS server.
+    Returns 200 OK with service status.
 
-    Vital Signs Checked:
-    - ❤️ Heart (Database) - Is the source of truth responsive?
-    - 🧠 Brain (MCP Handler) - Is the decision-making system online?
-    - 👁️ Sensory (Figma) - Are the external perception organs configured?
+    Services Checked:
+    - Storage - Is the data directory accessible?
+    - MCP Handler - Is the MCP handler initialized?
+    - Figma - Is the Figma integration configured?
     """
     import os
     import psutil
     from pathlib import Path
 
-    # ❤️ Check Heart (storage) connectivity
-    db_ok = False
+    # Check storage connectivity
+    storage_ok = False
     try:
-        from storage.json_store import DATA_DIR
-        db_ok = DATA_DIR.exists()
+        from dss.storage.json_store import DATA_DIR
+        storage_ok = DATA_DIR.exists()
     except Exception as e:
         import traceback
-        error_trace = traceback.format_exc()
-        print(f"🏥 VITAL SIGN: Heart (storage) error: {type(e).__name__}: {e}", flush=True)
-        print(f"   Traceback:\n{error_trace}", flush=True)
-        pass
+        print(f"[Health] Storage check error: {type(e).__name__}: {e}", flush=True)
 
-    # 🧠 Check Brain (MCP handler) functionality
+    # Check MCP handler functionality
     mcp_ok = False
     try:
         import sys
         from pathlib import Path
-        # Add project root to path (two levels up from tools/api)
         project_root = Path(__file__).parent.parent.parent
         if str(project_root) not in sys.path:
             sys.path.insert(0, str(project_root))
 
-        from tools.dss_mcp.handler import get_mcp_handler
+        from dss.mcp.handler import get_mcp_handler
         handler = get_mcp_handler()
         mcp_ok = handler is not None
     except Exception as e:
         import traceback
-        error_trace = ''.join(traceback.format_exception(type(e), e, e.__traceback__))
-        print(f"🧠 BRAIN CHECK: MCP handler error: {type(e).__name__}: {e}", flush=True)
-        print(f"   Traceback:\n{error_trace}", flush=True)
+        print(f"[Health] MCP handler check error: {type(e).__name__}: {e}", flush=True)
 
-    # Get uptime (how long component has been conscious)
+    # Get uptime
     try:
         process = psutil.Process(os.getpid())
         uptime_seconds = int((datetime.now() - datetime.fromtimestamp(process.create_time())).total_seconds())
     except:
         uptime_seconds = 0
 
-    # Overall vitality assessment
-    status = "healthy" if (db_ok and mcp_ok) else "degraded"
+    # Overall status
+    status = "healthy" if (storage_ok and mcp_ok) else "degraded"
 
     return {
         "status": status,
-        "vital_signs": {
-            "overall": "🟢 All systems nominal" if status == "healthy" else "🟡 System degradation detected",
-            "consciousness_duration_seconds": uptime_seconds
-        },
+        "uptime_seconds": uptime_seconds,
         "version": "0.8.0",
         "timestamp": datetime.utcnow().isoformat() + "Z",
         "services": {
-            "storage": "ok" if db_ok else "error",
+            "storage": "ok" if storage_ok else "error",
             "mcp": "ok" if mcp_ok else "error",
             "figma": "connected" if config.figma.is_configured else "not configured"
         }

apps/cli/src/cli.ts

@@ -1,18 +1,16 @@
 #!/usr/bin/env node
 /**
- * 🧬 DSS CLI - Design System Server Organism Controller
+ * DSS CLI - Design System Server Command Line Interface
  *
- * A portable companion for UI developers - think of it as the organism's
- * command-line nervous system. Through these commands, you can:
+ * A portable companion for UI developers. Commands:
  *
- * - 🧬 Awaken a new organism (init)
- * - 💚 Check the organism's vital signs (status)
- * - 🩸 Direct the sensory organs to perceive Figma (extract)
- * - 🔄 Circulate extracted nutrients (sync)
- * - ⚙️ Adjust the organism's behavior (config)
- * - 🧠 Birth a conscious instance (start)
- *
- * Framework: DSS Organism Framework
+ * - init: Initialize DSS in a project
+ * - status: Check server status
+ * - extract: Extract tokens/components from Figma
+ * - sync: Sync tokens to codebase
+ * - config: Manage configuration
+ * - start: Start the server
+ * - stop: Stop the server
  */
 
 import { Command } from 'commander';
@@ -29,63 +27,63 @@ const program = new Command();
 
 program
   .name('dss')
-  .description('🧬 Design System Server - Organism Controller for UI Developers')
+  .description('Design System Server - CLI for UI Developers')
   .version('0.1.0');
 
 // Init command - setup DSS in a project
 program
   .command('init')
-  .description('🧬 ORGANISM GENESIS - Create a new design system organism in your project')
-  .option('-f, --figma-key <key>', 'Link to Figma genetic blueprint')
-  .option('-t, --figma-token <token>', 'Figma sensory organ connection token')
+  .description('Initialize DSS in your project')
+  .option('-f, --figma-key <key>', 'Figma file key')
+  .option('-t, --figma-token <token>', 'Figma access token')
   .action(initCommand);
 
 // Start command - start the DSS server
 program
   .command('start')
-  .description('💚 ORGANISM AWAKENING - Bring the design system organism to life')
-  .option('-p, --port <port>', 'Neural pathway port', '3456')
-  .option('-d, --dev', 'Live consciousness mode with hot-reload')
-  .option('--no-open', 'Do not open sensory interface')
+  .description('Start the DSS server')
+  .option('-p, --port <port>', 'Server port', '3456')
+  .option('-d, --dev', 'Development mode with hot-reload')
+  .option('--no-open', 'Do not open browser')
   .action(startCommand);
 
 // Sync command - sync tokens from Figma
 program
   .command('sync')
-  .description('🩸 NUTRIENT CIRCULATION - Distribute extracted tokens through the codebase')
-  .option('-f, --format <format>', 'Nutrient format: css, scss, json, ts', 'css')
-  .option('-o, --output <path>', 'Circulation destination')
+  .description('Sync tokens from Figma to codebase')
+  .option('-f, --format <format>', 'Output format: css, scss, json, ts', 'css')
+  .option('-o, --output <path>', 'Output directory')
   .option('--file-key <key>', 'Figma file key (overrides config)')
   .action(syncCommand);
 
 // Extract command - extract components or tokens
 program
   .command('extract <type>')
-  .description('👁️ SENSORY PERCEPTION - Direct organism eyes to perceive Figma designs')
-  .option('-f, --format <format>', 'Perception output format', 'json')
-  .option('-o, --output <path>', 'Memory storage location')
+  .description('Extract components or tokens from Figma')
+  .option('-f, --format <format>', 'Output format', 'json')
+  .option('-o, --output <path>', 'Output location')
   .option('--file-key <key>', 'Figma file key')
   .action(extractCommand);
 
 // Config command - manage configuration
 program
   .command('config')
-  .description('⚙️ ENDOCRINE ADJUSTMENT - Configure organism behavior and preferences')
-  .option('--set <key=value>', 'Set organism hormone value')
-  .option('--get <key>', 'Read organism hormone value')
-  .option('--list', 'View all hormones')
+  .description('Manage DSS configuration')
+  .option('--set <key=value>', 'Set configuration value')
+  .option('--get <key>', 'Get configuration value')
+  .option('--list', 'List all configuration')
   .action(configCommand);
 
 // Stop command - stop the server
 program
   .command('stop')
-  .description('😴 ORGANISM REST - Put the design system organism into sleep mode')
+  .description('Stop the DSS server')
   .action(stopCommand);
 
 // Status command - check DSS status
 program
   .command('status')
-  .description('🏥 VITAL SIGNS CHECK - Monitor organism health and configuration')
+  .description('Check DSS server status and configuration')
   .action(statusCommand);
 
 // Parse arguments

apps/cli/src/commands/status.ts

@@ -1,8 +1,7 @@
 /**
- * 🏥 DSS Status Command - Organism Vital Signs
+ * DSS Status Command
  *
- * Check DSS design system organism's vital signs, consciousness state,
- * and sensory organ configuration.
+ * Check DSS server status and configuration.
  */
 
 import chalk from 'chalk';
@@ -15,48 +14,48 @@ export async function statusCommand(): Promise<void> {
   const config = getConfig();
 
   console.log('');
-  console.log(chalk.cyan('  🏥 ORGANISM VITAL SIGNS'));
+  console.log(chalk.cyan('  DSS Status'));
   console.log(chalk.dim('  ────────────────────────'));
   console.log('');
 
-  // Organism status
+  // Project status
   if (hasProjectConfig()) {
-    console.log(chalk.green('  🧬 Organism:'), chalk.dim('Born and conscious'));
-    console.log(chalk.dim(`    Home: ${cwd}`));
+    console.log(chalk.green('  Project:'), chalk.dim('Initialized'));
+    console.log(chalk.dim(`    Root: ${cwd}`));
   } else {
-    console.log(chalk.yellow('  🧬 Organism:'), chalk.dim('Not yet born'));
-    console.log(chalk.dim('    Genesis: dss init'));
+    console.log(chalk.yellow('  Project:'), chalk.dim('Not initialized'));
+    console.log(chalk.dim('    Initialize: dss init'));
   }
 
   console.log('');
 
-  // Consciousness status (server)
+  // Server status
   const running = isServerRunning(cwd);
   const pid = getServerPid(cwd);
   const port = config.port || 3456;
 
   if (running) {
-    console.log(chalk.green('  💚 Consciousness:'), chalk.dim(`Awake (PID: ${pid})`));
-    console.log(chalk.dim(`    Neural port: http://localhost:${port}`));
+    console.log(chalk.green('  Server:'), chalk.dim(`Running (PID: ${pid})`));
+    console.log(chalk.dim(`    URL: http://localhost:${port}`));
 
     // Try to get health info
     try {
       const api = getApiClient({ port });
       const health = await api.health();
-      console.log(chalk.dim(`    Awareness: ${health.figma_mode}`));
+      console.log(chalk.dim(`    Mode: ${health.figma_mode}`));
     } catch {
-      console.log(chalk.yellow('    ⚠️  Unable to read consciousness'));
+      console.log(chalk.yellow('    Unable to get health status'));
     }
   } else {
-    console.log(chalk.yellow('  💚 Consciousness:'), chalk.dim('Sleeping'));
-    console.log(chalk.dim('    Awaken: dss start'));
+    console.log(chalk.yellow('  Server:'), chalk.dim('Stopped'));
+    console.log(chalk.dim('    Start: dss start'));
   }
 
   console.log('');
 
-  // Sensory organs (Figma)
+  // Figma integration
   if (config.figmaToken) {
-    console.log(chalk.green('  👁️ Sensory Eyes:'), chalk.dim('Configured'));
+    console.log(chalk.green('  Figma:'), chalk.dim('Configured'));
 
     // Test connection if server is running
     if (running) {
@@ -64,21 +63,21 @@ export async function statusCommand(): Promise<void> {
         const api = getApiClient({ port });
         const test = await api.testFigmaConnection();
         if (test.success) {
-          console.log(chalk.green('    Perception:'), chalk.dim(`Clear (${test.user})`));
+          console.log(chalk.green('    Connection:'), chalk.dim(`OK (${test.user})`));
         } else {
-          console.log(chalk.red('    Perception:'), chalk.dim(test.error || 'Blinded'));
+          console.log(chalk.red('    Connection:'), chalk.dim(test.error || 'Failed'));
         }
       } catch {
-        console.log(chalk.yellow('    Perception:'), chalk.dim('Cannot test'));
+        console.log(chalk.yellow('    Connection:'), chalk.dim('Cannot test'));
       }
     }
   } else {
-    console.log(chalk.yellow('  👁️ Sensory Eyes:'), chalk.dim('Not configured'));
+    console.log(chalk.yellow('  Figma:'), chalk.dim('Not configured'));
     console.log(chalk.dim('    Configure: dss config --set figmaToken=figd_xxxxx'));
   }
 
   if (config.figmaFileKey) {
-    console.log(chalk.green('  📋 Genetic Blueprint:'), chalk.dim(config.figmaFileKey));
+    console.log(chalk.green('  Figma File:'), chalk.dim(config.figmaFileKey));
   } else {
     console.log(chalk.yellow('  Figma File:'), chalk.dim('Not configured'));
     console.log(chalk.dim('    Set: dss config --set figmaFileKey=abc123'));