feat: Support configuration via flags, env vars and config file

[irvinlim]

Revamps configuration handling for the application.

• Supports configuration via environment variables (fixes Configure with environment variables #37) as well as configuration files (preferred way moving forward).
• Revamp configuration handling to merge down configuration in the following order of precedence (from lowest to highest):
  • Configuration file (JSON and YAML both supported)
  • Environment variable
  • Command-line flags
• Refactor existing command-line flags to unified entrypoint, and add notice to avoid adding too many superfluous command-line flags moving forward.
  • Currently I have not yet decided which flags (if any) shall be marked as deprecated, which should show a warning or error if we choose to fully deprecate them in the future, but may be considered for future plans to reduce maintenance burden.