Jira backend refactor

[sallyom]

@Gkrumbach07 @cooktheryan don't be scared - this is a beautiful thing & it works!! The jira integration isn't quite there yet but I'd like to merge this first and keep working on that. I've added Gage to all commits since this is a huge refactor moving our code around.

Summary:

  components/backend/
  ├── crd/                    # Custom Resource Definition helpers
  │   └── rfe.go             # RFE workflow CR operations
  ├── git/                    # Git operations
  │   └── operations.go      # Clone, push, diff, GitHub integration
  ├── github/                 # GitHub authentication
  │   ├── app.go            # GitHub App integration
  │   └── token.go          # Token management
  ├── handlers/               # HTTP request handlers (organized by domain)
  │   ├── content.go        # Content service endpoints
  │   ├── github_auth.go    # GitHub OAuth handlers
  │   ├── health.go         # Health check endpoint
  │   ├── helpers.go        # Shared handler utilities
  │   ├── middleware.go     # Authentication & context middleware
  │   ├── permissions.go    # RBAC permission management
  │   ├── projects.go       # Project CRUD operations
  │   ├── repo.go           # Repository operations
  │   ├── rfe.go            # RFE workflow handlers
  │   ├── secrets.go        # Secret management
  │   └── sessions.go       # Agentic session lifecycle
  ├── jira/                   # Jira integration
  │   └── integration.go    # Jira API client & publishing
  ├── k8s/                    # Kubernetes resource definitions
  │   └── resources.go      # GVR definitions for CRDs
  ├── server/                 # Server initialization
  │   ├── k8s.go           # K8s client setup & config
  │   └── server.go        # HTTP server & routing
  ├── types/                  # Shared type definitions
  │   ├── common.go        # Common types & utilities
  │   ├── project.go       # Project-related types
  │   ├── rfe.go           # RFE workflow types
  │   └── session.go       # Session types
  ├── websocket/              # WebSocket messaging
  │   ├── handlers.go      # WebSocket HTTP handlers
  │   └── hub.go           # WebSocket hub & message persistence
  ├── main.go                 # Application entry point
  ├── go.mod                  # Go module definition
  ├── go.sum                  # Dependency checksums
  ├── Makefile                # Build & development tasks
  ├── Dockerfile              # Production container image
  ├── Dockerfile.dev          # Development container image
  ├── JIRA_NOTES.md          # Jira integration documentation
  └── REFACTOR_NOTES.md      # Refactor progress tracking


  Key improvements from refactor:
  - Organized handlers by domain (was 3906-line monolith)
  - Extracted packages: crd, git, github, jira, k8s, server, types, websocket
  - Separated concerns: routing, initialization, business logic
  - Improved testability and maintainability
  - No functional changes (except Jira enhancements)

[Gkrumbach07]

Trust the process

/approve

Y'all get ready for the frontend version