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Found and fixed a couple more places where file reference tags weren't being updated, and moved it all to one method in FileReference.

Found and fixed a couple more places where file reference tags weren't being updated,
and moved it all to one method in FileReference.
@deboer-tim deboer-tim merged commit 17c2313 into icpctools:main Sep 18, 2025
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@deboer-tim deboer-tim deleted the file-tag branch September 18, 2025 11:37
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