docs(readme): clarify what `init -i` does vs plain `init` (#483) (#545)

A user asked what the `-i` flag does and why it isn't the default. Add a short
note under the Initialize Projects quickstart: plain `init` only scaffolds the
`.codegraph/` dir, `-i`/`--index` also runs the first index, and without it you
run `codegraph index` afterwards.

Co-authored-by: Claude Opus 4.8 (1M context) <noreply@anthropic.com>