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storage: don't modify the given cfg.Opts
This change improves the `NewPebble` code to not modify the given `cfg.Opts`. Such behavior is surprising and can trip up tests that reuse the same config. Also, `ResolveEncryptedEnvOptions` and `wrapFilesystemMiddleware` no longer modify the Options directly; and `CheckNoRegistryFile` is now a standalone function. Release note: None Epic: none
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