Update scripts/run_ci.sh to cover directories in the exercises dir

Right now `scripts/run_ci.sh` will test everything in the root of the project, but now that we split README.md to sub-directories, it requires us to update `scripts/run_ci.sh` accordingly

Read scripts/run_ci.sh and inspect how the exercises directory is organized after README.md was split into subdirectories. Update the script so its CI run covers the exercises in those directories, then verify that the script tests both root-level and nested exercise content.

Written by the indexing model from the issue text.