A full graphify update evicted every edge whose source_file was a
re-extracted source, including LLM semantic edges (e.g.
semantically_similar_to) from Markdown docs that also have an AST
extractor. The AST pass cannot regenerate those edges, so they were
silently lost while their concept nodes survived — node eviction is
provenance-aware via _origin (#1116), edge eviction was not.
Tag AST-extracted edges with the same _origin=ast marker nodes already
carry, and scope rebuild-driven edge eviction to that tier: re-extraction
replaces a source's AST edges, while its semantic edges survive until a
semantic re-extraction supersedes them. Deletion-driven eviction stays
provenance-blind, so edges of deleted or excluded sources are still
purged regardless of tier.
Edges from graphs built before this change lack the marker; a stale
AST edge from a file changed exactly once between the old and new
version can linger until its source is deleted — the same migration
trade-off the #1116 node marker made.
xor_xe
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