Generate h5ai-nginx patch consistently

[acuarica]

We currently use IntelliJ to generate the h5ai-nginx, but it seems it can reorder previously applied changes when introducing a small change. #100 (comment)

We should generate the patch in a way that does not reorder changes. We may use git add . && git diff --staged to generate the patch. Moreover, this way it is reproducible and we can automate it if needed.