Improve tests

[Navarro-Jonathan]

Integration test improvements
These changes will test all commands through the CLI. Before, the integration tests were mostly smoke testing the program using a few different commands.

• Added tests for all commands and sub-commands for models, plans, configurations, constraints, expansions, metadata, scheduling, and constraints.
• Added tests for commands that download files
• Removed /'s in paths to support multiple platforms
• Improved simulation tests--we now use "real" configs and run additional simulations after updating the plans.
• Improved documentation
• Improved test structure--split tests into multiple modules, moved session handling into conftest.py.