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/wiggle/test-helpers/Cargo.toml

@@ -19,7 +19,7 @@ wiggle = { path = "..", features = ["tracing_log"] }
 thiserror = "1.0"
 tracing = "0.1.26"
 tracing-subscriber = "0.3.1"
-env_logger = "0.8"
+env_logger = "0.9"
 
 [badges]
 maintenance = { status = "actively-developed" }