>The most frustrating part of using Clippy is that it did not force a reanalysis of all packages in my cargo workspace when invoked multiple times.

This is because the author used `#[warn(clippy::all)]` instead of `#[deny]`. Warnings do not fail the build, so subsequent rebuilds will be no-ops. If you're at the stage where you've fixed regular compilation errors and are only fixing clippy lints, you should probably change that to `#[deny]`. (I personally keep it at `#[deny]` from the start.) Or run clippy as `cargo clippy -- -Dwarnings` to treat warnings as errors.

>Linking to code units in rustdoc was hard to do correctly since there were so many ways to do it.

If you're planning to publish the crate to crates.io and are okay with relying on docs.rs to host the docs, then you can rely on the fact that docs.rs uses a nightly rustdoc and use nightly-rustdoc-specific features. Specifically you can use

    [`Foo`]

to create a link to whatever `Foo` happens to be in the code scope.

>My one complaint is that `RUST_LOG=debug cargo run` dumps all of the verbose debug logs from cargo while your program is being built.

You would use the env_logger builder to parse a different env var like "PUNCHTOP_LOG", instead of the default "RUST_LOG".