`insertEdge` has always used `INSERT OR IGNORE`, but the edges table carried
no UNIQUE constraint — only an autoincrement PK and non-unique indexes — so
`OR IGNORE` had nothing to conflict on and behaved like a plain INSERT.
Whenever two extraction/resolution passes emitted the same edge (e.g. a
return type captured by both a type-reference and a value-reference pass),
the graph stored byte-identical duplicate rows: ~527 on this repo, inflating
edge counts and letting callers/impact list the same relationship twice.
Add a UNIQUE identity index on (source, target, kind, IFNULL(line,-1),
IFNULL(col,-1)) — in schema.sql for fresh databases and migration v6 (dedup
existing rows, then create the index) for existing ones. IFNULL folds the
nullable line/col so coordinate-less edges (synthesized / file-level) dedup
too; SQLite otherwise treats each NULL as distinct. Distinct call sites
(same source/target/kind, different line/col) are preserved — only
byte-identical structural duplicates collapse. This is the storage-layer
invariant the reporter identified: it makes OR IGNORE keep its promise and
catches every double-emit, present and future, rather than chasing each
emitting pass.
Migration v6 is deterministic (keeps the lowest id per identity group) and
idempotent (IF NOT EXISTS index; no-op DELETE once unique). The DELETE's
GROUP BY matches the index expression exactly so creation can't fail on a
leftover pair.
Co-authored-by: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
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