Add native support for multiple `org_path` in modules and subworkflows directories

Description of feature

As discussed with @edmundmiller and the infrastructure team at the Boston Hackathon 2024. Neuroimaging modules and subworkflows in nf-core will live aside of the nf-core directories, in modules/neuroimaging and subworkflows/neuroimaging. However, the current framework doesn't support it, tools need to be adapted for modules and subworkflows.

Here is a (non-exhaustive yet) list of potential problems :

• Linting and testing locally is not possible without changing org_path in .nf-core.yml
• Installation in pipelines is not possible without changing org_path in .nf-core.yml
• Lint and test checks fail since they cannot discover the modules and subworkflows correctly (names are not mangled correctly since they don't contain nf-core)

A good use-case of this is the first neuroimaging PR nf-core/modules#5673 . An equivalent of the modules in that PR are also in nf-scil. There the tests and linting passes (we did many changes on our end to do so); they are a good reference.

The issue names .nf-core.yml, local lint and test checks, installation, and the nf-core/modules#5673 and nf-scil references. Start by tracing how org_path is read and used by module and subworkflow discovery, naming, linting, testing, and installation. Done means multiple org_path values work without editing .nf-core.yml and the neuroimaging layouts pass those checks.