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This is a cleanup-only/documentation change, no behavior changes.

Add comments explaining how Directory locking works.

Move protected methods to private (there was no reason for them to be
protected).

Move private data members below private method declarations.

For methods that take a ScopedKernelLock, always pass by const reference
before non-const pointer parameters.

Give ClearDirtyMetahandles a ScopedKernelLock parameter so it's clear
that the caller must be holding a lock.

BUG=

Review URL: https://codereview.chromium.org/585663002

Cr-Commit-Position: refs/heads/master@{#296045}