use explicit dependencies in src/app

[ylecornec]

This PR sets (implicit_transitive_deps false) in the dune-project files of src/app,
adds the necessary explicit dependencies and removes some unnecessary ones.

Explain how you tested your changes:

• dune build in the affected folders
• The CI failure seems unrelated

• make build
  make build_all_sigs
  make build_archive
  make build_archive_all_sigs
  make build_rosetta
  make build_intgtest
  

Checklist:

• Modified the current draft of release notes with details on what is completed or incomplete within this project
• Document code purpose, how to use it
  • Mention expected invariants, implicit constraints
• Tests were added for the new behavior
  • Document test purpose, significance of failures
  • Test names should reflect their purpose
• All tests pass (CI will check this if you didn't)
• Serialized types are in stable-versioned modules
• Does this close issues? List them

[lk86]

LGTM but you will have to resolve the conflicts and get CI to pass, whether the failure is related or not