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fix: preserve files during filesystem copies - #1178
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andiwand
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Both output repositories carry the pdf-annotation.js from #1171 and #1173. A full run on 078390a matched every reference page byte for byte; only that script changed. #1178, merged since, changes how a file copy is written, not its bytes. Co-Authored-By: Claude Opus 5.5 (1M context) <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01MxyTMutqSUJRGfxA8CyzMc
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Copying a file onto itself truncated it before reading; a failed source read also destroyed an existing destination. Route filesystem copies through the existing atomic writer, closing the source before replacement. This also reuses checked flush and cleanup behavior.
Validation: filesystem regressions failed before the fix and pass afterward; Filesystem.* and VirtualFilesystem.* pass in the integrated stack. Atomic replacement changes inode identity and requires write access to the destination directory.
Stack: based on
main. Review against this base; merge the stack bottom-up.