Refactor code organization to follow domain-based approach

[coderabbitai]

Description

Currently, the codebase follows a pattern where code is organized by type:

• Custom types in the types module
• FromProof implementations in proof.rs
• Query implementations in query.rs, etc.

As discussed in PR #2449, this approach can become inconvenient as the codebase grows, since related functionality is spread across different files.

Proposed Solution

Refactor the codebase to follow a domain-based approach where related functionality is grouped together by domain/feature rather than by type.

Benefits

• Improved developer experience by having related code in the same location
• Better code organization for a large project
• Easier to understand and maintain domain-specific functionality

References

• PR discussion