Improve readability of setting pipeflow options

[dad616610]

Improve readability and maintainability of pipeflow_setup

This PR simplifies the pipeflow initialization logic by:

1. Making deepcopy operations explicit and singular

   • Replaces hidden deepcopies in _iteration_check and _check_mode
   • Eliminates duplicate copying by centralizing the operation

2. Clarifying option precedence

   • Uses explicit {**a, **b} syntax for option merging
   • Clearly defines overwrite order

3. Removing redundant parameters

   • Deletes unused default parameters from pipeflow function definition
   • (Parameters were always overwritten by locals())

4. Applying DRY principle

   • Replaces repetitive branching in _iteration_check with loop logic
   • Reduces code duplication across mode checks

Additional improvements:

• Added tests for _iteration_check functionality

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Planned follow-up work (separate PRs):

1. Replace logging.* calls with warnings.warn for:

   • More appropriate user notifications
   • Single-session message suppression
   • Standard Python warning controls

2. Add parameter validation in init_options to:

   • Surface incorrect values earlier
   • Provide precise error location
   • Improve debugging feedback