Update documentation

[standage]

This PR updates the user manual to provide a more thorough treatment of the new end-to-end workflow. Various improvements were also made to the manual, the user demo, and various other pieces of documentation. They're all linked together, with an explanation of the purpose of each document.

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• Changes are clearly described above
• Any relevant issue threads are referenced in the description
• Any new features are tested (see the development manual for details)
• CLI documentation (see docs/cli.md) and Python API documentation (see microhapulator/api.py) are up-to-date and in sync
• Substantial changes are documented in CHANGELOG.md (see https://keepachangelog.com/en/1.0.0/)