Bootstrap override manifests path

[clementd64]

Manifests are generated inside a subpath named after the target namespace.
https://github.com/fluxcd/flux2/blob/v2.0.1/pkg/manifestgen/install/install.go#L86

However for better organisation, I usually put all cluster specific manifests inside a manifests subfolder (like ./clusters/foo/manifests/system/flux)

Can you consider allowing this path configuration ?

I can try to do a PR but didn't have knowledge on the code base and possible side effect.