Update to clap 3.* (#4082)

* Update to clap 3.0

This commit migrates all CLI commands internally used in this project
from structopt/clap2 to clap 3. The intent here is to ensure that we're
using maintained versions of the dependencies as structopt and clap 2
are less maintained nowadays. Most transitions were pretty
straightforward and mostly dealing with structopt/clap3 differences.

* Fix a number of `cargo deny` errors

This commit fixes a few errors around duplicate dependencies which
arose from the prior update to clap3. This also uses a new feature in
`deny.toml`, `skip-tree`, which allows having a bit more targeted
ignores for skips of duplicate version checks. This showed a few more
locations in Wasmtime itself where we could update some dependencies.

cranelift/Cargo.toml

@@ -41,7 +41,7 @@ indicatif = "0.13.0"
 thiserror = "1.0.15"
 walkdir = "2.2"
 anyhow = "1.0.32"
-structopt = "0.3.17"
+clap = { version = "3.1.12", features = ["derive"] }
 
 [features]
 default = ["disas", "wasm", "cranelift-codegen/all-arch", "souper-harvest"]