YAML files were classified as documents, so code-only / AST-only runs
(graphify update) produced zero nodes from them. Move .yaml/.yml into the
code path like .json: add a PyYAML-based structural extractor (extract_yaml)
registered in _DISPATCH, add the suffixes to CODE_EXTENSIONS, drop them from
DOC_EXTENSIONS and the splittable-text set.
Deterministic ids derived from the file path; top-level and nested keys become
nodes with contains edges, capped at 500 pairs / depth 6 to avoid exploding on
data-heavy YAML.
(cherry picked from commit 2e5565a684)