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Describe use and architecture of llm_transform.py flow #702

@gpsaggese

Description

@gpsaggese

We want to document llm_transform.py

I started the doc in the branch #703

[ ] Read the documentation on how we document (diataxis, etc)
./docs/documentation_meta/all.diataxis.explanation.md
./docs/documentation_meta/all.writing_docs.how_to_guide.md
./docs/documentation_meta/all.architecture_diagrams.explanation.md

[ ] Write a reference doc about how llm_transform.py works (use ./docs/tools/all.llm_transform.reference.md as a basis)

./dev_scripts_helpers/llms/dockerized_llm_apply_cfile.py
./dev_scripts_helpers/llms/llm_apply_cfile.py
./dev_scripts_helpers/llms/dockerized_llm_transform.py
./dev_scripts_helpers/llms/llm_transform.py

[ ] Write an howto doc (use ./docs/tools/all.llm_transform.how_to_guide.md)

E.g.,

> llm_transform.py -i research_amp/causal_kg/scrape_fred_metadata.py -o research_amp/causal_kg/scrape_fred_metadata.py.new -p code_fix_from_imports

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