Change outdir and savedir to not use pkgdir

[imreddyTeja]

All uses of pkgdir to specify save or output paths now use generate_output_path.

Purpose

Closes #545

To-do

Content

• output paths previously determined by pkgdir now use generate_output_path
• only remaining pkdir calls are used for includes

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• [x] I have read and checked the items on the review checklist.