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A new flag EncryptionDirectoryFactory.isIndexEnabled() is set when the EncryptionDirectory opens an output/input stream that requires encryption. For example, this may allow some custom code to log whether the index is encrypted.

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Just a general comment: It's pretty confusing/difficult (impacting ease of code review and observability -- that you are trying to add here) to have a Directory, named EncryptionDirectory no less, that can flip flop between being encrypted and not encrypted. IMO it'd be much easier for an EncryptionDirectory to be, well, encrypted -- period. Going from cleartext to encrypted could be done via backup/restore or via maybe even through the process of adding replicas (and removing the old), provided these go via the Directory. The DirectoryFactory would have to pick what it's a factory of when initializing a new directory. But that's not how things are...

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