Consolidate cli command code into a separate folder

[fel1x-developer]

What does this PR do?

Currently, commands that are directly and indirectly executed coexist in src/cli folder. This has two problems:

1. There are too many files with file name ending *_command.zig
2. When adding a new command or importing files under src/cli, it is hard to know if a command is directly executed by users. (e.g. run is directly executed by bun run while pack does not. There is no bun pack command)

When there is bun <command>, the code that executes the command is in src/cli/<command>.zig, with exception of bunx/bun x which is under src/cli/bunx.zig, not src/cli/x.zig.

• Documentation or TypeScript types (it's okay to leave the rest blank in this case)
• Code changes

How did you verify your code works?

Build success on Ubuntu 24.04.1 LTS WSL kernel 6.12.8

[RiskyMH]

there seems to be build fails https://buildkite.com/bun/bun/builds/9461#019457ef-3ea6-4cda-b536-d2c5544b9d39

[RiskyMH]

moving these files may cause issues with how the site redirects and other linkings to github raw

[fel1x-developer]

I don't have access to the code for https://bun.sh because it is closed source.
For documentation files, I finished following grep in bun repository.

$ grep -inr --include \*.md "_command.zig"
$ grep -inr --include \*.md "src/cli/"

[fel1x-developer]

Propably caused by: src/codegen/bundle-modules.ts

Is it prohibited to have two zig files with same filename? If it is, this is a huge issue in DX.