Apply clippy fixes

[tim-hoffman]

• Applied fixes suggested by "cargo clippy"
• A few of the suggestions were ignored by adding "allow" annotations to avoid changing public interfaces. These can be revisited in the future to assess the impact of minor changes to public interfaces.
• Box::clone followed by immediate de-reference is changed to first reference the value out of the box and clone only that value to avoid cloning the Box itself.
• Also a few other minor formatting changes and code simplifications.