Update clap and other dependencies

Summary of the updates:
- Clap v3 has been released and this PR updates to use it. I did a
`cargo upgrade` to update all the other dependencies, but if you
prefer me just updraing clap, I can go ahead and do that.
- Use assert_cmd for testing cli. This gives a cargo_bin method which
is more convenient for integration tests rather than doing cargo run.

Cargo.toml

@@ -12,24 +12,25 @@ keywords = ["continuous-integration", "secrets", "encryption"]
 categories = ["command-line-utilities"]
 
 [dependencies]
-aho-corasick = "0.7"
-anyhow = "1"
-clap = "~3.0.0-beta.2"
-env_logger = "0.9"
-fs-err = "2.6"
-log = "0.4"
-once_cell = "1.8"
-serde = { version = "1", features = ["derive"] }
-serde_yaml = "0.8.17"
-serde_json = "1.0.66"
+aho-corasick = "0.7.18"
+anyhow = "1.0.52"
+clap = { version = "3.0.0", features = ["derive", "env"]}
+env_logger = "0.9.0"
+fs-err = "2.6.0"
+log = "0.4.14"
+once_cell = "1.9.0"
+serde = { version = "1.0.132", features = ["derive"] }
+serde_yaml = "0.8.23"
+serde_json = "1.0.73"
 sodiumoxide = "0.2.7"
 
 [build-dependencies]
-anyhow = "1"
-vergen = { version = "5.1.1", default-features = false, features = ["git"] }
+anyhow = "1.0.52"
+vergen = { version = "6.0.0", default-features = false, features = ["git"] }
 
 [dev-dependencies]
-tempfile = "3"
+assert_cmd = "2.0.2"
+tempfile = "3.2.0"
 
 [profile.release]
 panic = "abort"