_rebuild_code fed Markdown/doc files (.md/.mdx/.qmd/.skill) into the AST
quick-scan while _reconcile_existing_graph preserved the same docs'
semantic (LLM) nodes, so every semantic-backed doc was represented twice
(heading nodes + concept nodes) and the graph bloated ~4x vs the CLI
`graphify . --update` path.
Semantic now supersedes AST per doc source: before choosing
extract_targets, read the existing graph's source identities that carry
semantic doc nodes (non-_origin=="ast", gated on file_type=="document"
so pre-#1865 marker-less graphs aren't misread) and exclude those docs
from the quick-scan in both the full-rebuild and changed_paths branches.
They stay in code_files, so the #1795 fail-closed corpus check and the
shrink accounting still cover them — a previously-bloated graph
self-heals on the next full rebuild (the AST ownership rule drops the
stale heading nodes) without the shrink guard refusing the smaller
write. On incremental rebuilds the excluded docs never enter
rebuilt/node-evicted identities, mirroring #1865's tier-scoped edge rule
at the node level, so a doc's semantic nodes and edges survive. Docs
with no semantic layer (and brand-new docs) keep the no-LLM quick-scan
structure from #09b33b7.
safishamsi
76f5bc98fe