refactor analysisparameters metadata to be flat and add line_start line_stop to all radon functions.

[cudmore]

Work on @src/kymflow_core/kym_file.py radon analysis parameters and @src/kymflow_core/metadata.py AnalysisParameters.

1. right now, analysis parameters has a structure like this:
   """
   "analysis_parameters": {
   "algorithm": "mpRadon",
   "parameters": {
   "window_size": 16,
   "start_pixel": null,
   "stop_pixel": null,
   "use_multiprocessing": true
   },
   "analyzed_at": "2025-11-20T06:01:10.639839+00:00",
   "result_path": null
   }
   """

I want to move remove the 'parameters' key and put all its keys like window_size, start_pixel, etc into the main analysis parameters data class (for example, at the same level as 'algorithm'.

2. This will change how we save and then load a @src/kymflow_core/kym_file.py @src/kymflow_core/metadata.py.

Our unit test data in @DaTa do not have any saved analysis (no json files). When we run the tests, perform analysis and save analyssi (all in a temp folder). I want a new unit test to ensure all fields programatically declared in AnalysisParameters are actually saved to the json file.

3. I want to expand @src/kymflow_core/kym_file.py analyze_flow():
   """
   def analyze_flow(
   self,
   window_size: int,
   *, # boundary between positional and keyword-only arguments
   start_pixel: Optional[int] = None,
   stop_pixel: Optional[int] = None,
   progress_callback: Optional[ProgressCallback] = None,
   is_cancelled: Optional[CancelCallback] = None,
   use_multiprocessing: bool = True,
   ) -> None:

"""

To include 2 new parameters like:
start_line: Optional[int] = None,
stop_line: Optional[int] = None,

3.1 we then need to add these parameters to the @src/kymflow_core/metadata.py AnalysisPArameters (like we have start_pixel and stop_pixel)

Recap:

For now we are not really using the concept of start/stop pixel or start/stop line. In a future github issue I will explain a refactor to use these to analyze a rectangular ROI of a kymfile tif np image. This will require adding line parameters to @src/kymflow_core/kym_flow_radon_gpt.py mp_analyze_flow()

4. add the same parameters to mp_analyze_flow()
   start_line: Optional[int] = None,
   stop_line: Optional[int] = None,

make sure we chose defaults based in n_time (like stop pixel uses n_space)

5. start_line and stop_line also have to be added to @src/kymflow_core/metadata.py AnalysisParameters.