refactor: move more commands to internal/cmd (#207)

* refactor: move more commands to internal/cmd

Part of https://github.com/ooni/probe/issues/1335.

We would like all commands to be at the same level of engine
rather than inside engine (now that we can do it).

* fix: update .gitignore

* refactor: also move jafar outside engine

* We should be good now?

internal/engine/.gitignore

@@ -2,9 +2,7 @@
 /.vscode
 /apitool
 /asn.mmdb
-/badproxy.pem
 /ca-bundle.pem
-/cmd/jafar/badproxy.pem
 /country.mmdb
 /example.org
 /jafar