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>

README.md

@@ -55,6 +55,8 @@ cd your-project
 codegraph init -i
 ```
 
+<sub>`codegraph init` just creates the local `.codegraph/` index directory; adding `-i` (`--index`) also builds the initial graph in the same step. Without `-i`, run `codegraph index` afterwards to populate it.</sub>
+
 <div align="center">
 
 ![1_C_VYnhpys0UHrOuOgpgoyw](https://github.com/user-attachments/assets/f168182f-4d9a-44e0-94d7-08d018cc8a3a)