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/src/cat.rs

@@ -5,19 +5,19 @@
 
 use crate::utils::read_to_string;
 use anyhow::{Context, Result};
+use clap::Parser;
 use cranelift_reader::parse_functions;
 use std::path::{Path, PathBuf};
-use structopt::StructOpt;
 
 /// Outputs .clif file
-#[derive(StructOpt)]
+#[derive(Parser)]
 pub struct Options {
     /// Specify input file(s) to be used. Use '-' for stdin.
-    #[structopt(required(true), parse(from_os_str))]
+    #[clap(required = true)]
     files: Vec<PathBuf>,
 
     /// Enable debug output on stderr/stdout
-    #[structopt(short = "d")]
+    #[clap(short)]
     debug: bool,
 }