Provide an option that allows Deno to ignore non-existent workspace members or to do so automatically

[eavidy]

My project (ProjectMain) uses git submodules to reference another repository's deno project (ProjectA). ProjectA has its
own deno.json. I added ProjectA to the workspace of ProjectMain.

The deno.json of ProjectMain

{
  "workspace": ["core", "project_a"]
}

If I run deno, I get some warnings, such as
Warning "nodeModulesDir" field can only be specified in the workspace root deno.json file.. However, I cannot modify
the deno.json of the sub-modules. I hope deno can automatically ignore it. Or provide some option to ignore it.

Another issue is that if I don't clone the submodules (sometimes submodules are not necessary), I won't be able to run
Deno in the workspace directory, and the Deno language server in VSCode won't start either.