build: explicitly add dependency include dir for header generation

Neovim and the generated headers needs to use the same include
directories to build correctly. However, we need to generate headers
before all target dependencies has been resolved, meaning that we cannot
rely on any target to determine the final list of include directories.
This may lead to a problems when bundling some, but not all or none,
dependencies as the dependency include directory won't be included.

Also remove the dependency path options as this assumes a specific
structure on the dependency build directory.

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