Refactor embedding into python tool, refresh documentation

[lachlanharrisdev]

Description

Refactored the embedding code from messy C gluing to a slightly cleaner & more robust python script. Also fixed the documentation to only include what's already in scope.

Checklist

Please ensure the following before requesting a merge:

• I have read and agree to the repository's CONTRIBUTING.md and LICENSE.md.
• All tests pass locally (make, make test).
• Relevant documentation has been updated (README.md, docs/).
• Code follows the repository's style and formatting guidelines.
• I have added/updated relevant tests.

Related Issues

None provided.

Additional Notes

None provided.

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