Major refactor: Consolidate DSS into unified package structure

- Create new dss/ Python package at project root
- Move MCP core from tools/dss_mcp/ to dss/mcp/
- Move storage layer from tools/storage/ to dss/storage/
- Move domain logic from dss-mvp1/dss/ to dss/
- Move services from tools/api/services/ to dss/services/
- Move API server to apps/api/
- Move CLI to apps/cli/
- Move Storybook assets to storybook/
- Create unified dss/__init__.py with comprehensive exports
- Merge configuration into dss/settings.py (Pydantic-based)
- Create pyproject.toml for proper package management
- Update startup scripts for new paths
- Remove old tools/ and dss-mvp1/ directories

Architecture changes:
- DSS is now MCP-first with 40+ tools for Claude Code
- Clean imports: from dss import Projects, Components, FigmaToolSuite
- No more sys.path.insert() hacking
- apps/ contains thin application wrappers (API, CLI)
- Single unified Python package for all DSS logic

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

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

tests/test_project_analyzer.py

@@ -0,0 +1,45 @@
+import pytest
+import json
+from pathlib import Path
+from dss.analyze.project_analyzer import run_project_analysis
+
+def test_run_project_analysis(mock_react_project: Path):
+    """
+    Tests the run_project_analysis function to ensure it creates the analysis graph
+    and that the graph contains the expected file nodes.
+    """
+    # Run the analysis on the mock project
+    run_project_analysis(str(mock_react_project))
+
+    # Check if the analysis file was created
+    analysis_file = mock_react_project / ".dss" / "analysis_graph.json"
+    assert analysis_file.exists(), "The analysis_graph.json file was not created."
+
+    # Load the analysis data
+    with open(analysis_file, 'r') as f:
+        data = json.load(f)
+
+    # Verify the graph structure
+    assert "nodes" in data, "Graph data should contain 'nodes'."
+    assert "links" in data, "Graph data should contain 'links'."
+
+    # Get a list of node IDs (which are the relative file paths)
+    node_ids = [node['id'] for node in data['nodes']]
+
+    # Check for the presence of the files from the mock project
+    expected_files = [
+        "package.json",
+        "src/App.js",
+        "src/components/ComponentA.css",
+        "src/components/ComponentA.jsx",
+        "src/components/ComponentB.tsx",
+    ]
+
+    for file_path in expected_files:
+        # Path separators might be different on different OSes, so we normalize
+        normalized_path = str(Path(file_path))
+        assert normalized_path in node_ids, f"Expected file '{normalized_path}' not found in the analysis graph."
+
+    # Verify the number of nodes
+    # There should be exactly the number of files we created
+    assert len(node_ids) == len(expected_files), "The number of nodes in the graph does not match the number of files."