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codeintel: Ensure paths respect root when checking existence in git

Warren Gifford requested to merge pci-existence-check-with-root into master

Created by: efritz

Forgot to prepend the root into paths when checking their existence in git. Currently any LSIF upload with a non-nil root will evict all contents as it doesn't think any of the files exist in the repo.

This now matches the previous behavior.

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