feat(cli): codegraph init builds the initial index by default (#483) (#546)

`codegraph init` now runs the initial index automatically. The -i/--index
flag is kept but is now a no-op, accepted for backward compatibility so
existing muscle memory and scripts don't break. Addresses #483, where a user
asked why -i wasn't implicit.

README and site/ docs are intentionally NOT updated in this commit — they
describe the currently-released 0.9.7 behavior (where -i is still required).
Update them at the 0.9.8 release so users on 0.9.7 aren't misled.

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