Refactor config/plugin compatibility paths to Python 3.12 and remove legacy parsing duplication

[Copilot]

This change removes remaining legacy compatibility branches and anti-pattern typing around config/plugin loading. It centralizes config-file parsing through the core model path and aligns runtime behavior with the project’s Python 3.12 minimum.

All PR-Submissions:

---

• Have you followed the guidelines in our Contributing document?
• Have you checked to ensure there aren't other open
  Pull Requests for the same
  update/change?

New ✨✨ Feature-Submissions:

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• Does your submission pass tests?
• Have you lint your code locally prior to submission? Fixed:
• This PR is for a new feature, not a bug fix.

Changes to ⚙️ Core-Features:

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• Have you added an explanation of what your changes do and why you'd like
  us to include them?

• Have you written new tests for your core changes, as applicable?

• Have you successfully run tests with your changes locally?

• Problem addressed

  • Remaining anti-patterns: untyped legacy bridges (Any/casts), duplicated core vs Jupyter parsing paths, and Python <3.12 compatibility code still present in active paths.

• Core changes

  • Python 3.12 standardization
    • Replaced tomli reads with stdlib tomllib in:
      • spectrafit/core/fitting_config.py
      • spectrafit/cli/commands/convert.py
      • spectrafit/models/project_config.py
    • Removed tomllib/tomli import fallback branches in Jupyter config loading and corresponding unit test path.
  • Eliminated core/Jupyter parsing duplication
    • spectrafit/jupyter/config_io.py::load_notebook_config() now validates through UnifiedFittingConfig.from_file(...) instead of re-implementing file parsing.
  • Removed plugin discovery anti-pattern
    • spectrafit/plugins/discovery.py now uses entry_points().select(...) directly; removed cast("Any", ...), plugins_eps: Any, and old-version branching.
  • Focused regression coverage
    • Added tests/unit/test_plugin_discovery.py for entry_points().select(...) discovery behavior.
    • Updated tests/unit/test_jupyter_roundtrip.py to use tomllib directly.

• Representative change

  # before (duplicated parser path in jupyter/config_io.py)
  if src.suffix == ".toml":
      raw = tomllib.load(fh)
  elif src.suffix == ".json":
      raw = json.load(fh)
  return UnifiedFittingConfig.model_validate(raw)
  
  # after (single core parser/validator path)
  if src.suffix not in {".toml", ".json"}:
      raise ValueError(...)
  return UnifiedFittingConfig.from_file(src)

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[semanticdiff-com]

Review changes with  

Changed Files

File	Status
spectrafit/plugins/discovery.py	30% smaller
tests/unit/test_jupyter_roundtrip.py	23% smaller
spectrafit/jupyter/config_io.py	10% smaller
spectrafit/cli/commands/convert.py	0% smaller
spectrafit/core/fitting_config.py	0% smaller
spectrafit/models/project_config.py	0% smaller
tests/unit/test_plugin_discovery.py	0% smaller

[sonarqubecloud]

Quality Gate passed

Issues
1 New issue
0 Accepted issues

Measures
0 Security Hotspots
0.0% Coverage on New Code
0.0% Duplication on New Code

See analysis details on SonarQube Cloud

[stale]

This pull request has been automatically marked as stale because it has not had recent activity. It will be closed if no further activity occurs. Thank you for your contributions.