Mention some file dependencies of dune files explicitly

[georgeee]

Explicitly mention a few implicit file dependencies in dune files.

Also contains some changes to how bash scripts are called from Dune (via explicit Bash call), this simplifies usage in nix wrapping and seems to do no harm to default flow.

Explain how you tested your changes:

• Mina compiles

Checklist:

• [x] Dependency versions are unchanged
  • Notify Velocity team if dependencies must change in CI
• [x] Modified the current draft of release notes with details on what is completed or incomplete within this project
• [x] Document code purpose, how to use it
  • Mention expected invariants, implicit constraints
• [x] Tests were added for the new behavior
  • Document test purpose, significance of failures
  • Test names should reflect their purpose
• [x] All tests pass (CI will check this if you didn't)
• [x] Serialized types are in stable-versioned modules
• [x] Does this close issues? None

[mrmr1993]

!ci-build-me