WASM incremental build drops edges (442 missing vs full build)

[carlos-alm]

Description

When running a WASM incremental build with 5 changed files, the resulting graph has 442 fewer edges than a full build of the same codebase. This means incremental rebuilds silently produce an incomplete graph.

Reproduction

# Full build baseline
codegraph build src --engine wasm --no-incremental
# Output: 10,695 nodes, 21,461 edges

# Touch 5 files
echo "// change" >> src/cli.ts
echo "// change" >> src/domain/parser.ts
echo "// change" >> src/db/index.ts
echo "// change" >> src/domain/queries.ts
echo "// change" >> src/domain/graph/builder.ts

# Incremental rebuild
codegraph build src --engine wasm
# Output: 10,695 nodes, 21,019 edges  ← 442 edges MISSING

Expected

Incremental build should produce the same edge count as a full build (21,461 edges).

Observed

• Full build: 21,461 edges
• Incremental (5 files): 21,019 edges (-442)

Context

• Native engine does NOT have this bug — incremental produces 21,534 edges (slight increase from comment lines is expected)
• WASM incremental also reparses 87 reverse-dep files beyond the 5 changed (see WASM incremental reparses reverse-dep files unnecessarily (92 vs 5) #933), which may be related — edges from those files may not be correctly re-inserted
• Version: 3.9.4-dev.8, Windows 11, Node 22.18.0

Impact

Users relying on WASM incremental builds get silently degraded query results — missing call edges, broken impact analysis, incorrect dead-code detection.