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fix(toolkit): avoid EMFILE and preserve mode when zipping (#3428)
To preserve file order using `archiver` files must be appended serially either using stream or buffer (appending by file path does not preserve order even when done serially). Appending using buffer seems to be the only way to solve `EMFILE` errors. Call `fs.stat` before appending to preserve mode. Closes #3145, Closes #3344, Closes #3413
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