Fix agent runtime parsing failures and restore automatic workflow execution

[madhavikodale]

Problem:
Agents fail during execution with:

• Failed to parse claude JSON output
• no live execution path

Impact:

• Tasks remain blocked
• Agents fail to auto-complete workflows
• Automatic document generation fails
• Issues are not closing automatically

Goal:

• stabilize runtime execution
• enforce structured JSON responses
• restore live execution paths
• enable automatic workflow completion and issue auto-closing