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graph: same clobber class as #787 in env-access CONFIGURES sources and resolve_file_throws #842

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@DeusData

Follow-up disclosed during #828's review (stable USAGE-edge ownership): the same latent bug class — shared directory-module nodes having name/file_path/props clobbered by whichever same-package file processes last, and unguarded merge_update_existing relabeling — also affects the env-access CONFIGURES source attribution and resolve_file_throws. #828 deliberately scoped to USAGE edges; port the same guard + per-file File-node fallback to these two sites, with an #828-style multi-order red fixture.

Refs #787, #828.

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    bugSomething isn't workingparsing/qualityGraph extraction bugs, false positives, missing edgespriority/normalStandard review queue; useful PR with ordinary maintainer urgency.

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