Refactor code directory structure

Context

Restructure and clean up the code directory.

Summary

• Move all unused code to legacy directory (used to be old)
• Create analysis_data directory for classes such as Event, Pulse, Waveform, Baseline
• Update paths for files that have moved
• Change baseline to baseline_processing to match other directory names (pulse_analysis, pulse_finding)
• Make sub-directories in reader directory to hold classes for each type of reader (v1730, v1740)
• Reformat Makefile to have shorter lines

How was this tested?

The code compiles and runs as it did before.