Move shared Platform code to separate modules

[jorgee]

This pull request introduces modularization improvements to the Nextflow project and decouples some classes based on the usage of Nexflow classes in Platform

Enhancements

• Decouple AssetManager and ConfigBuilder from cli package:
  • Define interfaces ConfigNodeOption, ConfigRunOptions and ConfigCliOptions to access the required options from ConfigBuilder without requiring the rest of cli classes
  • Same for HubOptions, it is now an interface at scm package and implement in cli as CliHubOptions
• Remove NF class dependency from ConfigBuilder
  • DSL parser version can be moved to Const as it is just a Environment Variable inspection.
  • ConfigBuilder includes a strict flag to indicate when to use strict mode when merging maps.
• Remove HistoryFile dependency from ConfigBuilder
  • Move normalizeResumeId to CmdRun. It is only used when the cmdRun field is set. Use ConfigRunOptions interface to get the normalized resume id value.
• Move the classes to the new modules based on the functionality, we propose to create 3 new modules:
  • nf-secrets: contains the current secret package in the nextflow module and nextflow.util.SecretHelper class. Depends on nf-commons
  • nf-config: contains the current config package in the nextflow module and the nextflow.util.ConfigHelper class. Depends on nf-secrets and nf-commons
  • nf-scm: contains the current scm package in the nextflow module and the nextflow.script.ScriptFile class. Depends on nf-config and nf-commons
• Move classes to nf-commons:
  • Some exceptions, nexflow.executor.BashTemplate and nextflow.util.MustacheTemplateEngine: used by Platform
  • nextflow.ast.NextflowXForm: required by config parsers
  • nextflow.parser.v2.ErrorListener: required by ConfigParserV2

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[bentsherman]

Thanks @jorgee for looking into this. Let's focus on your codebase analysis for now, as we need to agree on a plan first

I suspect if we finalize #5971 and make a few judgement calls, we can make this work with fewer changes. But I need to study your analysis first.

Once we agree on a plan, we can add it here as an ADR.

[pditommaso]

Apart the previous comment, massive PR, well done!

[pditommaso]

Please avoid all not strictly required changes. We can make this kind of refactor in a followup pr