53 replace keepout flag by general tagging

[rpahl]

This pull request refactors the pipeline step metadata to replace the keepOut parameter with a new tags parameter across the codebase. The tags parameter allows associating custom tags with each step, enabling more flexible selection or skipping of steps based on tags. All references to keepOut have been removed from both the implementation and documentation, and example code has been updated accordingly.

The most important changes are:

API and Data Structure Changes:

• The keepOut parameter has been removed from both the Pipeline class and related alias functions. Instead, a new tags parameter (character vector) is introduced to allow tagging steps for later selection or filtering. All internal uses and documentation of keepOut have been replaced with tags. [1] [2] [3] [4] [5] [6] [7]

Documentation and Example Updates:

• All Roxygen and inline code examples have been updated to use the new tags parameter instead of keepOut. Example outputs now often use |> str() to show structure, reflecting modern R idioms. [1] [2] [3] [4] [5] [6] [7] [8] [9] [10] [11] [12] [13] [14]

Internal Implementation Adjustments:

• The pipeline's internal data frame and related logic have been updated to store and process tags instead of keepOut. All code paths that referenced keepOut (such as step addition, replacement, and output collection) have been migrated to use the new tagging mechanism or have been simplified. [1] [2] [3] [4] [5]

This update modernizes and generalizes the pipeline step metadata, making it easier to manage and select steps by arbitrary tags rather than a single boolean flag.