Update developer docs for Direct transfer

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This is a follow-up from !114921 (comment 1322163624) We should update our Direct transfer documentation with the following information:

1. Explain the NDJSON pipelines
2. Explain how the source instance generates the NDJSON files
3. Explain project migrations
4. Update the diagram

/cc @rodrigo.tomonari @georgekoltsov @m_frankiewicz