Deprecate and remove lesser-used API methods for JctFileManager and Workspace

[ascopes]

We have lots of methods in classes like Workspace which will rarely ever be used, such as:

• addPatchModulePathModule
• addUpgradeModulePathModule
• addNativeHeaderOutputModule
• addSystemModulePathModule

etc.

To keep the API simple, deprecate these methods (and remove them entirely in the v1.0.0 branch).

Users can call .addModule(Location, String) or similar instead going forwards on the offchance they actually need to use these.

[ascopes]

Closed by GH-418