Refactor repository layout to separate application code, generated assets, runtime state, and python support apps

[slbotbm]

Currently, the repository is mixing Go entrypoints, Go packages, eBPF source, generated bindings, config templates, and mutable runtime file in overlapping directories. This makes the project unintuitive to a first time user, as well as harder to maintain due to the accumulation of non-conventional repository structural choices. Further, the information required to run the project is scattered in multiple readme's, which makes it difficult to run the project from scratch for a first time user.

I would like to make the following changes:

• move executable go entry point into top-level cmd/.
• move application-internal Go packages to top-level internal/.
• move shared wire/config/result types into internal/protocol/.
• move native helper sources into dedicated cmd/ subdirectories and build outputs into bin/
• move eBPF source into internal/simulator/bpf/ and headers into internal/simulator/headers/
• move checked-in demo configs into configs/simulator/demos/
• keep client/ and dashboard/ top-level
• rename data/ to analysis/

Resulting directory structure:

  river/
  ├── cmd/
  │   ├── river/
  │   │   └── main.go
  │   ├── injector/
  │   │   └── main.c
  │   └── state-injector/
  │       └── main.c
  ├── bin/
  │   ├── river
  │   ├── injector
  │   └── state-injector
  ├── internal/
  │   ├── server/
  │   ├── simulator/
  │   │   ├── bpf/
  │   │   │   └── probe.c
  │   │   ├── headers/
  │   │   │   └── vmlinux.h
  │   │   ├── gen.go
  │   │   ├── probe_bpfel.go
  │   │   ├── probe_bpfeb.go
  │   │   ├── probe_bpfel.o
  │   │   ├── probe_bpfeb.o
  │   │   └── simulator.go
  │   └── protocol/
  ├── configs/
  │   └── simulator/
  │       ├── demos/
  │       │   ├── M1_C1_config.json
  │       │   ├── M1_C2_config.json
  │       │   ├── M1_C3_config.json
  │       │   ├── M2_C1_config.json
  │       │   ├── M2_C2_config.json
  │       │   ├── M3_C1_config.json
  │       │   ├── M3_C2_config.json
  │       │   └── M3_C3_config.json
  │       └── README.md
  ├── docs/
  │   ├── architecture.md
  │   ├── development.md
  │   └── project-layout.md
  ├── external/
  │   └── README.md
  ├── client/
  ├── dashboard/
  ├── analysis/
  ├── simulator/
  │   ├── .gitignore
  │   ├── config.json
  │   └── _utils/
  ├── Makefile
  ├── go.mod
  ├── pyproject.toml
  ├── README.md
  └── CONTRIBUTING.md

cc @dariofad

[dariofad]

Hi, I agree it will improve the user experience, and I'd rather simplify the proposed structure even more (e.g., we still don't have a well defined protocol to interact with the server).
Currently, I'm in the middle of a large refactoring to enable multiple read and write operations, so I'd be happy to address this issue later. After pushing the changes I'll notify you. Thanks.