feat: support v2 sync protocol

[doc-han]

Description

This PR makes sync v2 protocol the default for syncing projects with Github. It still allows users to fallback to the old config.json style by explicitly enabling it.

Currently defaults to v2 but can be switched to v1 style

Closes #4523

Validation steps

1. Try to sync a project with github
2. You'll notice the default will push an openfn.yaml instead of openfn-<project-id>-config.json
3. Do an actual push to github
4. Check whether your openfn.yaml is in github with nicely generated content like the example below

Example openfn.yaml content

project:
  uuid: 43c34b65-50cf-4ec3-b480-32b3b17ac9c0
  endpoint: http://localhost:4000
  alias: 
  inserted_at: 2026-04-13T01:00:00Z
  updated_at: 2026-04-13T04:37:54Z
  id: sync
  name: sync
workspace:
  credentials: credentials.yaml
  dirs:
    projects: .projects
    workflows: workflows
  formats:
    openfn: yaml
    project: yaml
    workflow: yaml

Additional notes for the reviewer

1. (Is there anything else the reviewer should know or look out for?)

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[doc-han]

Problems

1. Why don't we allow users to generate a new github project from our platform when doing sync? (because if I need it on a new repo, I'll have to manually create that on github)
2. When a repo has no content yet. We're unable to find the branches on it. i.e we can't find main on the repo

[doc-han]

@josephjclark suggests we keep v1 as default and then allow users to switch to v2 style

[josephjclark]

This is a really nice idea, and we need to bank it because when we make v2 the default, this is probably how we'll want to handle it.

But for now we actually want to leave v1 the default until v2 has had a bit more testing.

[josephjclark]

Calling v1 "legacy" internally is still the correct thing to do though :)