Both git fast-paths in ExtractionOrchestrator (sync and getChangedFiles)
classified every untracked (`??`) file as "added" without checking the
index. Indexing a file doesn't make git track it, so the file stayed `??`
and was re-reported as pending and re-indexed on every run: `codegraph
status` listed it under Pending Changes forever and each `sync` re-added
it, even though its symbols were already queryable.
Merge the modified + added handling into a single hash-compared loop so
untracked files get the same treatment as tracked ones: "added" only if
missing from the index, "modified" if contents changed, skipped otherwise.
The non-git fallback path already did this and is unchanged.
Closes#206. Reported by @15290391025.
Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
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