docs: restructure README into grouped sections

Reorganize the README around six top-level sections (Features,
Installation, Usage, Configuration, Docker, Q&A, Development) so
related content is no longer scattered:

- add a table of contents
- move the long Motivation section to the end and lead with a
  one-line description
- collect all config topics (CLI overrides, startup banner,
  entrypoint, env files, platform overrides, watch rules) under
  Configuration
- collect all Docker topics (official image, shell function,
  Compose, custom Dockerfile) under Docker
- put each badge on its own line
- fix the missing line continuation in the docker run example,
  which made `-c <CONF>` parse as a separate command
- normalize Q&A headings, trailing whitespace and long lines

Author: xiantang