CHANGELOG.md
LICENSE
MANIFEST.in
README.md
VISION.md
install.sh
pyproject.toml
docs/index.md
docs/quickstart.md
docs/assets/images/CLI_Startup_Image.png
docs/concepts/agent_modes.md
docs/concepts/agents.md
docs/concepts/analysis_modes.md
docs/concepts/memory.md
docs/concepts/sessions.md
docs/concepts/tools.md
docs/concepts/ui.md
docs/guides/cli_usage.md
docs/guides/installation.md
docs/guides/session_based_usage.md
docs/implementation/BROWSER_OPTIMIZATION_COMPLETE.md
docs/implementation/COORDINATE_ARRAY_FIX.md
docs/implementation/ENHANCED_UI_INTEGRATION_SUMMARY.md
docs/implementation/ENHANCED_UI_USAGE.md
docs/implementation/FIXES_APPLIED.md
docs/implementation/ISSUES_FIXED_SUMMARY.md
docs/implementation/PROGRESS_REPORT.md
docs/implementation/SIMPLE_MEMORY_IMPLEMENTATION.md
docs/implementation/TEST_RESULTS_SUMMARY.md
docs/implementation/UI_ENHANCEMENT_IMPLEMENTATION_PLAN.md
docs/implementation/UI_ENHANCEMENT_SUCCESS_SUMMARY.md
docs/implementation/UNIFIED_INTERFACE_IMPLEMENTATION_SUMMARY.md
docs/implementation/session_based_solution.md
docs/reference/index.md
docs/reference/cli/index.md
docs/reference/config/index.md
docs/reference/errors/index.md
docs/tools/chemeleon.md
docs/tools/mace.md
docs/tools/smact.md
docs/tools/visualisation.md
examples/universal_cif_demo.py
src/crystalyse_ai/__init__.py
src/crystalyse_ai/__main__.py
src/crystalyse_ai/cli.py
src/crystalyse_ai/config.py
src/crystalyse_ai/converters.py
src/crystalyse_ai/unified_cli.py
src/crystalyse_ai.egg-info/PKG-INFO
src/crystalyse_ai.egg-info/SOURCES.txt
src/crystalyse_ai.egg-info/dependency_links.txt
src/crystalyse_ai.egg-info/entry_points.txt
src/crystalyse_ai.egg-info/requires.txt
src/crystalyse_ai.egg-info/top_level.txt
src/crystalyse_ai/agents/__init__.py
src/crystalyse_ai/agents/crystalyse_agent.py
src/crystalyse_ai/agents/mcp_utils.py
src/crystalyse_ai/agents/session_based_agent.py
src/crystalyse_ai/infrastructure/__init__.py
src/crystalyse_ai/infrastructure/mcp_connection_pool.py
src/crystalyse_ai/infrastructure/resilient_tool_caller.py
src/crystalyse_ai/infrastructure/session_manager.py
src/crystalyse_ai/mcp_servers/__init__.py
src/crystalyse_ai/mcp_servers/creative/__init__.py
src/crystalyse_ai/mcp_servers/creative/server.py
src/crystalyse_ai/mcp_servers/unified/__init__.py
src/crystalyse_ai/mcp_servers/unified/server.py
src/crystalyse_ai/mcp_servers/visualization/__init__.py
src/crystalyse_ai/mcp_servers/visualization/browser_pool.py
src/crystalyse_ai/mcp_servers/visualization/server.py
src/crystalyse_ai/mcp_servers/visualization/tools.py
src/crystalyse_ai/memory/__init__.py
src/crystalyse_ai/memory/cross_session_context.py
src/crystalyse_ai/memory/crystalyse_memory.py
src/crystalyse_ai/memory/discovery_cache.py
src/crystalyse_ai/memory/memory_tools.py
src/crystalyse_ai/memory/session_memory.py
src/crystalyse_ai/memory/user_memory.py
src/crystalyse_ai/output/__init__.py
src/crystalyse_ai/output/creative_formatter.py
src/crystalyse_ai/output/dual_formatter.py
src/crystalyse_ai/output/universal_cif_visualizer.py
src/crystalyse_ai/prompts/unified_agent_prompt.md
src/crystalyse_ai/tests/test_visualization.py
src/crystalyse_ai/tools/__init__.py
src/crystalyse_ai/tools/chemeleon.py
src/crystalyse_ai/tools/chemeleon_installer.py
src/crystalyse_ai/tools/dependency_checker.py
src/crystalyse_ai/tools/mace.py
src/crystalyse_ai/tools/smact.py
src/crystalyse_ai/tools/visualization.py
src/crystalyse_ai/ui/__init__.py
src/crystalyse_ai/ui/ascii_art.py
src/crystalyse_ai/ui/components.py
src/crystalyse_ai/ui/enhanced_cli.py
src/crystalyse_ai/ui/gradients.py
src/crystalyse_ai/ui/themes.py
src/crystalyse_ai/utils/__init__.py
src/crystalyse_ai/utils/chemistry.py
src/crystalyse_ai/utils/structure.py
src/crystalyse_ai/validation/__init__.py
src/crystalyse_ai/validation/response_validator.py