Incremental sync misses cross-file relations after a new export is added

[loadcosmos]

Summary

On CodeGraph v1.3.1, incremental sync can leave the graph semantically stale when a changed file introduces an export that satisfies an existing import/call in an unchanged file.

The index reports a clean state (pendingChanges = 0, pendingRefs = 0, state = "complete", reindexRecommended = false), but a full index of the exact same source snapshot adds missing edges.

Minimal TypeScript reproduction

Initial a.ts:

import { greet } from './b';

export function run(): number {
  return greet();
}

Initial b.ts:

export function other(): number {
  return 1;
}

1. Run a full initial index:

codegraph init --force .

2. Replace b.ts with:

export function greet(): number {
  return 42;
}

3. Run incremental sync and inspect the graph:

codegraph sync --quiet .
codegraph status --json .

Actual result after sync

• fileCount: 2
• nodeCount: 5
• edgeCount: 4
• edge kinds: contains: 3, imports: 1
• pendingChanges: { added: 0, modified: 0, removed: 0 }
• pendingRefs: 0

Then run a full index without changing any source file:

codegraph index --force --quiet .
codegraph status --json .

Result after full index

• fileCount: 2
• nodeCount: 5
• edgeCount: 6
• edge kinds: calls: 1, contains: 3, imports: 2
• pendingChanges: { added: 0, modified: 0, removed: 0 }
• pendingRefs: 0

Expected result

For an unchanged source snapshot, sync should produce the same resolved cross-file graph as a full index. In this case, the import/call in unchanged a.ts should be resolved after b.ts adds greet.

Impact

The MCP file watcher uses incremental sync, so impact, caller/callee, and flow results can silently omit cross-file relationships after a normal edit. Status does not indicate that a full re-index is needed.

This appears consistent with reference resolution being scoped to changed files: the unresolved reference in unchanged a.ts is not revisited after b.ts gains the matching export.

Environment

• CodeGraph: 1.3.1
• Linux x64
• TypeScript

[colbymchenry]

Thanks for the excellent report — the minimal repro made this a pleasure to chase down, and your diagnosis was exactly right: reference resolution was scoped to the changed files' refs, and a completed pass deleted every ref it failed to resolve, so the unresolved reference in unchanged a.ts was gone before b.ts ever gained greet. Nothing could revisit it short of a full re-index.

Fixed in #1249 (merged, ships in the next release):

• References that fail to resolve are now kept (parked as failed) instead of deleted, and every sync retries the ones whose name matches a symbol the changed files now carry. Your repro now produces a graph identical to a full index after sync — including calls and the second imports edge — and this also covers e.g. a class gaining a method that other files already call.
• The inverse hole is fixed too: when an edit removes or moves a symbol (or deletes its file), callers in unchanged files re-resolve during the same sync — rebinding to the symbol's new location, or reconnecting automatically when it comes back — instead of silently losing the edge.
• status stays honest throughout: parked refs don't show up as pending work, so a clean report now actually means the graph matches the source.

One note for existing indexes: the fix can't retroactively recover references an older version already discarded, so a one-time codegraph index --force after upgrading gets you a clean baseline — everything after that heals incrementally.