[colbymchenry]

Fixes #2565.

What was wrong

codegraph sync exits 1 with Failed to sync: FOREIGN KEY constraint failed in a project whose code lazy-loads a workspace package, and every later sync fails the same way. A full index of the same tree succeeds. @bompus's report bisects it to #2420 and pins the cause:

• lazyValueModules names the module a lazy value loads as a synthesis input, so a sync that changes the module redraws the JSX that names the value.
• For dynamic(() => import('icons').then((mod) => mod.EdgeFunctions)) (Supabase Studio), the resolver hands back the package directory, packages/icons. vben's () => import('@vben/layouts').then((m) => m.IFrameView) does the same in five apps.
• synthesis_inputs.file_path references files(path). The stage's publish step therefore fails on the directory, and the whole sync rolls back.

What changed

Both places that write synthesis_inputs now keep only paths the files table holds:

• QueryBuilder.replaceSynthesisInputs, which writes to the index directly;
• SynthesisStage.publish, inside its BEGIN IMMEDIATE write transaction. That also covers a file leaving the index while the passes run.

A directory never matched a changed file, so dropping it loses nothing.

Not in scope: resolving a workspace package's lazy import to its entry file. With that, the value would reach EdgeFunctions, and an edit to the entry would redraw it. Today the lookup reads the directory and finds nothing, before and after this change.

Tests (__tests__/sync-synthesis-inputs.test.ts)

• The issue's reproduction: a pnpm workspace, src/App.tsx lazy-loading icons, two syncs after edits, then the graph compared with a fresh index of the final tree.
• replaceSynthesisInputs keeps only indexed files (packages/icons and a deleted path dropped).
• SynthesisStage.publish keeps only indexed files, whatever reached the stage's own list.
• All three fail on main. Each of the two guards is killed by its own test when reverted alone.
• Full suite on main 3308cff + this change, with the native kernel: 7,538 passed, 0 failed, 80 skipped. After rebasing onto c65f9bb (fix(extraction): a build folder inside src/ is indexed for its Go and C# files too #2687, file discovery only), the 36 sync and synthesis test files and fix(extraction): a build folder inside src/ is indexed for its Go and C# files too #2687's test pass (256 tests).

A/B: main 3308cff vs this branch, native kernel built from the same source

• Fresh indexes: vben (61c0793), excalidraw (e1b7aac) and zod (afdac65) are byte-identical (scripts/dump-graph.mjs).
• vben sync: index, then append a line to the five apps/*/src/layouts/index.ts files, then codegraph sync.
  • main: exit 1, FOREIGN KEY constraint failed.
  • this branch: exit 0, and the synced graph equals a fresh index of the edited tree.

Credit

Reported and diagnosed by @bompus. @inth3shadows found the same cause and opened #2574 for it; this is our own implementation, and the CHANGELOG thanks both.

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