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.

crates/fuzzing/Cargo.toml

@@ -10,7 +10,7 @@ license = "Apache-2.0 WITH LLVM-exception"
 [dependencies]
 anyhow = "1.0.22"
 arbitrary = { version = "1.1.0", features = ["derive"] }
-env_logger = "0.8.1"
+env_logger = "0.9.0"
 log = "0.4.8"
 rayon = "1.2.1"
 target-lexicon = "0.12.3"