Clean up agent-service code structure and reconcile its types with the frontend

[bobbai00]

Task Summary

The agent-service/ (Bun/TS) codebase has accumulated structural inconsistencies that hurt readability and risk silent wire-contract bugs.

Code structure

Problem	Detail
Definitions scattered	~25 interfaces/types live in client/tool/util/server files instead of types/
Duplicate definitions	LogicalPlan / PortSchema / InputPortInfo defined twice; AgentSettingsApi is field-for-field identical to UpdateAgentSettingsRequest
Impure "clients"	api/ mixes HTTP clients with types, endpoint config, and JWT helpers; the execution HTTP client lives in agent/tools/, while api/execution-api.ts holds only types
Misleading naming	AgentDelegateConfig is a runtime binding (not config) and is re-declared inline 3× with conflicting shapes; *Config is used for non-config objects
Duplicate logic	jsonToTableFormat and the input/output-shape formatter are duplicated across two files

Inconsistency with the frontend wire contract

The agent reads/writes the same workflow and compile payloads as the Angular frontend, but several types/ definitions have drifted from frontend/src/app/.../*.interface.ts:

Type	agent-service (current)	frontend (source of truth)
CommentBox	{commentBoxID, comments: string, x, y, width, height}	{commentBoxID, comments: Comment[], commentBoxPosition: Point}
WorkflowSettings	missing executionMode	{dataTransferBatchSize, executionMode}
WorkflowFatalError	{type: string, message, operatorId?}	{message, details, operatorId, workerId, type: {name}, timestamp}

These avoid runtime breakage today only because the code reads a subset of the fields and passes the rest through opaquely — they are latent bugs, not correct shapes.

Task Type

• Refactor / Cleanup
• DevOps / Deployment / CI
• Testing / QA
• Documentation
• Performance
• Other