Working directory

You can set working directory by dir.

Let us assume a simple project structure

-/
-/src
-/src/main.c

Edit your neph.yml like this

main:
  command: |
    echo "Where am I?"
    pwd
  dir:
    src

The result of pwd is path_to_the_project/src, you can confirm the result at .neph/main/log/log.out by neph.