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/c-api/Cargo.toml

@@ -17,7 +17,7 @@ test = false
 doctest = false
 
 [dependencies]
-env_logger = "0.8"
+env_logger = "0.9"
 anyhow = "1.0"
 once_cell = "1.3"
 wasmtime = { path = "../wasmtime", default-features = false, features = ['cranelift', 'wasm-backtrace'] }