Revert "build: cleanup base files inclusion"

[Keno]

This change broke Revise. @JeffBezanson and I discussed this with a number of folks and the consensus was that:

1. We don't think the src/base thing really makes much sense.
2. We don't like not having symlinks, because that makes everything show up twice in grep and IDEs
3. Having Revise working is significantly more important than the original bug this fixed, which seems like it should be fixable by other Makefile improvements without touching the directory structure.

Reverts #45441.

[Keno]

Both Jeff and Jameson are on vacation now, but Jeff told me to do this in person, so I'll just consider than a review approval ;).