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An untracked nested repository makes gstack-cso start fail with UNSAFE_PATH. Git lists it as one entry with a trailing slash, so relativePath() rejected the empty segment and aborted the run. A registered submodule gitlink already failed one step later for the same reason: it is a directory, and the capture loop only reads regular files. Accept the boundary under its own name and record it like a host dependency tree: one manifest entry, originalHash not-read, an excluded: transformation that discloses the omission in the report's snapshot-inputs coverage, no payload copied, and an identity check during capture so a swapped or symlinked boundary fails closed. Nested repository contents are never audited with the outer repository because Git never descends into them.