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This is a major refactor of how env vars are handled. Previously, they were resolved as part of parsing but they really need to be done one at a time so that the results of each var can be used for the next one. This should also make it possible to greatly simplify how env vars are handled in tools by using the same logic.
Fixes #1262
Prereq for #1447
Prereq for #1303
Prereq for #1261