fix(sync): record only indexed files as synthesis inputs (#2565)

[inth3shadows]

Fixes #2565.

A lazy value that loads a workspace package by name, like dynamic(() => import('icons').then((mod) => mod.EdgeFunctions)), records the module it loads as a synthesis input (lazyValueModules, #2420). The import resolves a workspace package to its directory, packages/icons, which is not an indexed file. synthesis_inputs.file_path references files(path), so publishing the synthesis refresh failed with FOREIGN KEY constraint failed.

• Extraction had already committed, so only the synthesis refresh rolled back.
• synthesis_pending stayed set, so every later sync failed too, whichever file changed.
• A full index writes its inputs through the same replaceSynthesisInputs call and hit the same constraint. The synthesis step is best-effort there and swallows the error, so it left synthesis_inputs empty instead of failing.

Fix:

• One normalizing writer. replaceSynthesisInputs stores each input under the indexed file's own path and skips a path that is no indexed file. Paths are normalized first: a pass can be handed a module spelled the way its import wrote it (import('@/widgets/Chart/') gives src/widgets/Chart//index.ts, and a path can carry a ./ segment). Without that, a real file would be dropped and a later edit to it would never redraw.
• A re-check at publish. SynthesisStage.publish checks the staged inputs against files again inside its write lock, because they were staged before it took the lock.

Tests (verified) in __tests__/sync-synthesis-input-package.test.ts. All 4 fail on upstream/main and pass here:

• the issue's one-package pnpm workspace: the loading file is recorded after a full index, and a sync after editing it succeeds (on main: expected [] to …contain 'src/App.tsx', then FOREIGN KEY constraint failed);
• the issue's own trigger, an edit to another file with markup: the sync succeeds;
• a barrel imported as @/widgets/Chart/ or src/widgets/./Chart, then rewired: the barrel is recorded, and the synced render edges equal a fresh index's.

sync-lazy-route-value, sync-rebuild-convergence, migrations-synthesis-json, sync-jsx-import-forwarding and sync-nested-barrel-route still pass. Full suite on Linux / Node 22 (before the round-1 changes): Tests 1 failed | 6784 passed | 360 skipped (7145). The one failure, ui-server-api.test.ts > the engine's own busiest symbol, fails the same way on upstream/main in this checkout, because it reads a stale .codegraph here. This repo has no CI workflow that runs on pull requests.

Known limits (observed, and the same on main):

• Workspace packages resolve to a directory. The resolver returns the package directory, so the package's entry file (packages/icons/src/icons/index.ts) is never recorded as an input, and no edge is drawn from Chart to EdgeFunctions. Fixing that means resolving a workspace package through its main/exports and rejecting directories in import resolution. That is a wider change than this crash fix.
• Unindexed files. A pass can read a file that is on disk but not indexed, for example a gitignored barrel. It can't be recorded, because the column has a foreign key to files. If the file is indexed later, nothing marks it as an input until another refresh runs.

[colbymchenry]

Thanks @inth3shadows, this was the right diagnosis and the right fix. It landed as #2688, which filters synthesis inputs to indexed files at both places they're written: replaceSynthesisInputs and the stage's publish. You're credited in the CHANGELOG alongside @bompus's report. Closing this one as superseded, and thank you again.