refactor!: flatten crate organization to use workspace properly

[imrn99]

I consider this a breaking change since if people specified the dependency using a path, it will break.

This PR reorganize the crates of the repository to:

1. remove multiple nesting level
2. use the root manifest as a workspace manifest, unifying dependency spec across members

I could also move mesh-io/mesh-io-ffi to the tools crate to only keep coupe and tools visible at the root.

With this done, we can setup auto deps updates without PRs being too confusing.

Old structure

>tree --gitignore -L 2
.
├── Cargo.lock
├── Cargo.toml
├── Dockerfile
├── ..
├── benches
│   └── rcb_cartesian.rs
├── examples
│   └── simple.rs
├── ffi
│   ├── Cargo.toml
│   ├── src
│   └── ..
├── src
│   ├── lib.rs
│   ├── main.rs
│   └── ..
└── tools
    ├── Cargo.toml
    ├── ..
    ├── mesh-io
    ├── num-part
    ├── report
    └── src

New structure

>tree --gitignore -L 2
├── Cargo.lock
├── Cargo.toml
├── ..
├── coupe
│   ├── Cargo.toml
│   ├── benches
│   ├── examples
│   └── src
├── coupe-ffi
│   ├── Cargo.toml
│   ├── src
│   └── ..
├── mesh-io
│   ├── Cargo.toml
│   └── src
├── mesh-io-ffi
│   ├── Cargo.toml
│   ├── meshio.h
│   └── src
└── tools
    ├── Cargo.toml
    ├── ..
    ├── bins
    ├── lib
    ├── num-part
    └── report

[cedricchevalier19]

I think it makes a lot of sense to reorganize the repo like this.
Thank you