fix: Make submodule clone config an agent config

[DrJosh9000]

Description

BUILDKITE_GIT_SUBMODULE_CLONE_CONFIG was introduced in #1895 to fix a failing test, so it only made it as far as the job executor flags / env vars. Git config options are very powerful, so this should be controlled from the agent config.

Context

https://linear.app/buildkite/issue/A-987

Changes

• Add the same flag and env var to agent_start.go
• Propagate its value in job_runner.go:createEnvironment

Testing

• Tests have run locally (with go test ./...). Buildkite employees may check this if the pipeline has run automatically.
• Code is formatted (with go tool gofumpt -extra -w .)

Disclosures / Credits

I did not use AI tools at all

[swebb]

LGTM 👍