Refactor CLI

[janmasrovira]

Maintenance refactor of the app/ subtree.

Changes include:

1. commands are separated into modules to make it less cluttered.
2. Input files are no longer a global option, so completion and help work as intended.
3. Completion for input juvix files only suggest .juvix files.
4. Global flags must be given before any subcommand.
5. Now --output and --output-dir work with respect to where juvix is called and not the root of the project.
6. internal subcommand renamed to dev. It now shows in the utility commands help section instead of the compiler commands section.

[paulcadman]

Excellent - autocompletion of input filenames works again 🥳