Some typing and QOL fixes

[archermarx]

Fixes some type hinting and adds an optional prefix for output directories

Fixes

• Type errors eliminated in distributions.py, serialize.py, transform.py, and variable.py
• Many other typing issues resolved (many optional default assignments fixed to have correct "| None" type)
• Flaky tests on windows due to matplotlib trying to open interactive plots resolved by switching backend
• Loggers for Component and System now use null handlers when None to make sure we always have a valid Logger object

Features

• Add new args to loading a system from file: "timestamp_prefix" and "make_subdirs". The first allows you to change the name of the timestamped output file prefix from "amisc_" to something else, and the second disables the creation of timestamped subdirectories and dumps files directly in the specified root dir.