docs: clarify zero-config + built-in default-ignores; drop stale config wording (#418)

Refresh the README and docs-site Configuration pages to (a) state plainly there are no codegraph config files, (b) describe the new built-in default-ignores (#407) and the .gitignore-negation opt-in, and (c) remove the now-inaccurate note that committed vendor/dist dirs are indexed. Also fixes a stray 'excluded by config patterns' phrase in README troubleshooting.

Co-authored-by: Claude Opus 4.7 (1M context) <noreply@anthropic.com>