...
Build workflow must contain SCM plugin operations to extract source code for specific extension followed by this operation. This operation will find package.json file in extracted source to generate zip file appropriately. Generated zip file is saved as project version artifact in FlexDeploy, which will be used during Deploy workflow execution.
Your source code for extension may look like this. Parent folder structure does not matter as that is configurable in FlexDeploy project.
Environment/Instance Properties
...