Allow running pipelines from repository subfolders

[jorgee]

close #5890
This pull request updates the pipeline run logic to handle cases where the pipeline is specified in a subfolder of the URLs. The main changes involve passing the main script file to the AssetManager, updating its constructor and build method, and adding validation to prevent script files from being used as repository URLs.

Supported case:

$ nextflow run https://github.com/ekageyama/nextflow_sub -main-script pipeline/main.nf

 N E X T F L O W   ~  version 25.10.0

Pulling ekageyama/nextflow_sub ...
WARN: Cannot read project manifest -- Cause: Remote resource not found: https://api.github.com/repos/ekageyama/nextflow_sub/contents/nextflow.config
 downloaded from https://github.com/ekageyama/nextflow_sub.git
Launching `https://github.com/ekageyama/nextflow_sub` [stoic_wilson] DSL2 - revision: b409fabb25 [main]

executor >  local (2)
[7b/920f71] convertToUppercase | 1 of 1 ✔
[01/a45652] addPrefix          | 1 of 1 ✔
Pipeline completed at: 2025-11-21T19:49:05.875003740+01:00
Execution status: SUCCESS

However, it is not supporting passing the full URL path to the main script. The path parts dedicated to identify the repository depends on the type. The github case can be inferred, because they are always two, but not for the rest. Gitlab/Bitbucket/Gitea can be hosted and Azure can include 2 o 3 path parts. In this cases, now it prints this error

$ dev_nextflow run https://github.com/ekageyama/nextflow_sub/pipeline/main.nf

 N E X T F L O W   ~  version 25.10.0

Repository URL can end as a script file (.nf|.nxf) - Use -main-script option.

TODO:

• Undefined nextflow.config: should we look at repo root or in the main.nf location.
• Improve message error when not a valid repo. It currently report "Remote resource not found: https://api.github.com/repos/ekageyama/nextflow_sub/pipeline/contents/main.nf" which it can confuse as it seems a valid URL
• add unit tests

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[bentsherman]

Undefined nextflow.config: should we look at repo root or in the main.nf location

It should look for nextflow.config in the same directory as the main script