LLNL / spack / 4122

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Fixes #1720: spack reindex fails with invalid ref count.

- Database graph wasn't being built properly; dependencies were set up
  incorrectly in the nodes that ended up in the graph on reindex.

- Reworked _add to increment ref count properly and to always build
  bottom-up to make the logic simpler to understand.

32 of 32 new or added lines in 2 files covered. (100.0%)

7744 of 11975 relevant lines covered (64.67%)

0.65 hits per line