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>

dss/__init__.py

@@ -56,15 +56,14 @@ from dss.ingest.base import (
 
 # Export/Import
 from dss.export_import.service import DSSArchiveExporter, DSSArchiveImporter
-from dss.export_import.smart_merger import SmartMerger
+from dss.export_import.merger import SmartMerger
 
 # Storybook
 from dss.storybook.generator import StoryGenerator
 from dss.storybook.scanner import StorybookScanner
 
 # Translations
-from dss.translations.dictionary import TranslationDictionary
-from dss.translations.resolver import TokenResolver
+from dss.translations import TranslationDictionary, TokenResolver
 
 # Services
 from dss.services.project_manager import ProjectManager

dss/auth/atlassian_auth.py

@@ -12,7 +12,7 @@ from datetime import datetime, timedelta
 from typing import Optional, Dict, Any
 from atlassian import Jira, Confluence
 
-from storage.json_store import read_json, write_json, SYSTEM_DIR
+from dss.storage.json_store import read_json, write_json, SYSTEM_DIR
 
 
 class AtlassianAuth:

dss/export_import/merger.py

@@ -10,7 +10,7 @@ from .security import TimestampConflictResolver
 from ..models.project import Project
 from ..models.theme import DesignToken
 from ..models.component import Component
-from storage.json_store import Projects, Components, Tokens
+from dss.storage.json_store import Projects, Components, Tokens
 
 
 MergeStrategy = Literal["overwrite", "keep_local", "fork", "skip"]

dss/export_import/service.py

@@ -20,7 +20,7 @@ from .importer import DSSArchiveImporter, ImportAnalysis
 from .merger import SmartMerger, ConflictResolutionMode, MergeAnalysis
 from .security import DatabaseLockingStrategy, MemoryLimitManager
 from ..models.project import Project
-from storage.json_store import Projects, ActivityLog
+from dss.storage.json_store import Projects, ActivityLog
 
 
 @dataclass

dss/figma/figma_tools.py

@@ -19,18 +19,14 @@ Tools:
 import json
 import hashlib
 import asyncio
-import sys
 from datetime import datetime
 from typing import Optional, Dict, List, Any
 from dataclasses import dataclass, asdict
 from pathlib import Path
 import httpx
 
-# Add parent to path for imports
-sys.path.insert(0, str(Path(__file__).parent.parent))
-
-from config import config
-from storage.json_store import Cache, ActivityLog
+from dss.settings import settings
+from dss.storage.json_store import Cache, ActivityLog
 
 @dataclass
 class DesignToken:
@@ -67,9 +63,9 @@ class FigmaClient:
     """
 
     def __init__(self, token: Optional[str] = None):
-        self.token = token or config.figma.token
+        self.token = token or settings.FIGMA_TOKEN
         self.base_url = "https://api.figma.com/v1"
-        self.cache_ttl = config.figma.cache_ttl
+        self.cache_ttl = settings.FIGMA_CACHE_TTL
         self._use_real_api = bool(self.token)
 
     def _cache_key(self, endpoint: str) -> str:

dss/mcp/audit.py

@@ -11,7 +11,7 @@ from typing import Optional, Dict, Any
 from datetime import datetime
 from enum import Enum
 
-from storage.json_store import ActivityLog, append_jsonl, read_jsonl, SYSTEM_DIR  # JSON storage
+from dss.storage.json_store import ActivityLog, append_jsonl, read_jsonl, SYSTEM_DIR  # JSON storage
 
 
 class AuditEventType(Enum):

dss/mcp/context/project_context.py

@@ -17,7 +17,7 @@ from pathlib import Path
 import sys
 sys.path.insert(0, str(Path(__file__).parent.parent.parent))
 
-from storage.json_store import Projects, Components, Tokens
+from dss.storage.json_store import Projects, Components, Tokens
 from analyze.scanner import ProjectScanner
 from ..config import mcp_config
 

dss/mcp/handler.py

@@ -22,7 +22,7 @@ from pathlib import Path
 # Note: sys.path is set up by the importing module (server.py)
 # Do NOT modify sys.path here as it causes relative import issues
 
-from storage.json_store import Projects, ActivityLog
+from dss.storage.json_store import Projects, ActivityLog
 from .config import mcp_config, integration_config
 from .context.project_context import get_context_manager, ProjectContext
 from .tools.project_tools import PROJECT_TOOLS, ProjectTools

dss/mcp/integrations/base.py

@@ -12,7 +12,7 @@ from datetime import datetime, timedelta
 from enum import Enum
 
 from ..config import mcp_config
-from storage.json_store import Cache, read_json, write_json, SYSTEM_DIR
+from dss.storage.json_store import Cache, read_json, write_json, SYSTEM_DIR
 
 
 class CircuitState(Enum):

dss/mcp/operations.py

@@ -13,7 +13,7 @@ from datetime import datetime
 from enum import Enum
 
 from .config import mcp_config
-from storage.json_store import ActivityLog, read_json, write_json, DATA_DIR  # JSON storage
+from dss.storage.json_store import ActivityLog, read_json, write_json, DATA_DIR  # JSON storage
 
 
 class OperationStatus(Enum):

dss/mcp/security.py

@@ -16,7 +16,7 @@ from cryptography.hazmat.primitives.kdf.pbkdf2 import PBKDF2HMAC
 from cryptography.hazmat.backends import default_backend
 
 from .config import mcp_config
-from storage.json_store import read_json, write_json, SYSTEM_DIR  # JSON storage
+from dss.storage.json_store import read_json, write_json, SYSTEM_DIR  # JSON storage
 
 
 class CredentialVault:

dss/mcp/tools/project_tools.py

@@ -20,7 +20,7 @@ from mcp import types
 from ..context.project_context import get_context_manager
 from ..security import CredentialVault
 from ..audit import AuditLog, AuditEventType
-from storage.json_store import Projects, Components, Tokens, ActivityLog  # JSON storage
+from dss.storage.json_store import Projects, Components, Tokens, ActivityLog  # JSON storage
 from ..handler import get_mcp_handler, MCPContext
 
 

dss/services/project_manager.py

@@ -28,7 +28,7 @@ class ProjectManager:
         Initialize project manager.
 
         Args:
-            projects_db: Projects database class (from storage.database)
+            projects_db: Projects database class (from dss.storage.database)
             config_service: Optional ConfigService for config initialization
         """
         self.db = projects_db

dss/status/dashboard.py

@@ -190,7 +190,7 @@ class StatusDashboard:
 
         # Database stats
         try:
-            from storage.json_store import get_stats, ActivityLog, SyncHistory, Projects, Components
+            from dss.storage.json_store import get_stats, ActivityLog, SyncHistory, Projects, Components
 
             stats = get_stats()
             data.projects_count = stats.get("projects", 0)