Resolve Race Conditions

[alexplaka]

One of the simulation parameters was not thread safe. This PR fixes this issue.

Key Changes:

• Refactored regulated and Michaelis-Menten process methods to calculate transition probabilities in local variables instead of modifying the shared self.trans_p dictionary
• Added optional transition_p parameter to _order_0, _order_1, and _order_2 methods to accept pre-calculated transition probabilities
• Added Mermaid diagram documenting the simulation architecture

[Copilot]

Pull request overview

This PR resolves race conditions in the AbStochKin simulation when running in parallel mode by refactoring how transition probabilities are handled in regulated processes.

Key Changes:

• Refactored regulated process methods to calculate transition probabilities in local variables instead of modifying the shared self.trans_p dictionary
• Added optional transition_p parameter to _order_0, _order_1, and _order_2 methods to accept pre-calculated transition probabilities
• Added Mermaid diagram documenting the simulation architecture

Reviewed changes

Copilot reviewed 3 out of 3 changed files in this pull request and generated 3 comments.

File	Description
docs/simulation_architecture.mmd	New Mermaid flowchart documenting the simulation architecture and component relationships
abstochkin/agentstatedata.py	Reformatted np.concatenate call in __post_init__ for improved readability (no functional changes)
abstochkin/_simulation_methods.py	Resolved race condition by passing transition probabilities as parameters instead of modifying shared dictionary; updated 12 process-handling methods

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