Refactor `Mechanism`

[K20shores]

Refactor Mechanism in musica.mechanism_configuration to use Python wrapper classes consistently for reactions, species, and phases.

Acceptance Criteria

• Mechanism no longer inherits directly from _Mechanism.
• Holds internal instance _instance of _Mechanism.
• Constructor accepts Python-native objects: reactions (list of Python reaction classes), species (list of Python Species), phases (list of Python Phase), version (Python Version).
• reactions attribute wraps and manages internal C++ reaction objects but exposes Python reaction classes.
• to_dict() uses Python classes’ serialize() methods exclusively; no direct C++ class checks.
• Remove all direct C++ type checks; rely on Python class hierarchy or duck typing.
• export() uses MechanismSerializer.serialize passing the Python Mechanism instance.
• MechanismSerializer.serialize() validates type, creates directory, and writes JSON or YAML from to_dict() output.
• Raise errors for unsupported file formats and unsupported reaction types using Python classes.

Ideas

• Implement composition pattern: hold _Mechanism instance in self._instance.
• Map Python reaction classes in to_dict() instead of C++ types.
• Use isinstance checks with Python classes only.
• Avoid static methods for serialization; prefer instance methods.
• Handle version as a Python class member, not as a C++ member.

Tasks

• Change class Mechanism(_Mechanism) to class Mechanism holding self._instance.
• Update __init__ to accept Python reaction, species, phase, version objects and create _Mechanism instance internally.
• Refactor to_dict() to iterate Python-side lists and call their serialize() methods.
• Remove C++-type checks (_Arrhenius, _Branched, etc.); rely on Python class type checks.
• Update export() method to call MechanismSerializer.serialize(self, file_path).
• Modify MechanismSerializer.serialize() to accept Python Mechanism and use to_dict().
• Add proper error handling for unknown reaction types based on Python classes.