Expected Behavior

When building a project, md5 digests should only be calculated for files that are part of a rule (either input or target I assume).

Actual Behavior

Digests are calculated for files that are not part of any rule.

Reproduction

1. Create a new project with dune init project test && cd test
2. Check build time with time dune build @all:

   real	0m0.368s
   user	0m0.316s
   sys	0m0.218s
   

3. Create a very large file fallocate -l 10G elephant.img
4. Run build again with time dune build @all:

   real	0m45.851s
   user	0m35.427s
   sys	0m10.402s
   

By adding some logging I could check that it creates digests twice, for both test/elephant.img and _build/default/elephant.img.

Specifications

• Version of dune (output of dune --version): main branch (d75bd88), can reproduce as well with v 2.8.5 published in opam
• Version of ocaml (output of ocamlc --version): 4.12.0
• Operating system (distribution and version): Debian 10