Reduce proto CopyFrom for deeply nested structures

[ducky64]

Replaces it with populate_x, which is more efficient.

CopyFrom with a ref_map (or any other kind of dict) remains, the data there tends to be small so it's probably the least worst option.

Negligible effect on performance in practice.

Resolves #18

[Copilot]

Pull request overview

This PR refactors the protobuf serialization code to improve performance by replacing CopyFrom() calls with in-place population methods (populate_*) for deeply nested structures. The change eliminates the need to create temporary protobuf objects, instead populating them directly in their final destination.

Key changes:

• Replaced _expr_to_proto() with _populate_expr_proto() that takes a protobuf object to populate
• Replaced _decl_to_proto() with _populate_decl_proto() that populates in-place
• Replaced _instance_to_proto() with _populate_portlike_proto() that populates in-place
• Removed unused StructuredMetadata base class that is no longer needed

Reviewed changes

Copilot reviewed 8 out of 8 changed files in this pull request and generated no comments.

Show a summary per file

File	Description
edg/core/Ports.py	Updated Port classes to use _populate_portlike_proto() and _populate_decl_proto() methods instead of returning proto objects
edg/core/HierarchyBlock.py	Changed constraint and parameter initialization to use populate methods
edg/core/Core.py	Removed unused StructuredMetadata class and updated metadata type hints
edg/core/ConstraintExpr.py	Refactored expression types to use _populate_decl_proto() and _populate_expr_proto() with SetInParent() for optional fields
edg/core/Blocks.py	Updated block proto generation to use populate methods for parameters, ports, and constraints
edg/core/Binding.py	Comprehensive refactoring of all binding classes to use populate_expr_proto() and populate_literal_proto() methods; made ArrayBinding inherit from Binding instead of LiteralBinding
edg/core/ArrayExpr.py	Updated array expression proto generation to use populate methods
edg/core/Array.py	Updated array and vector proto generation to use _populate_portlike_proto()

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