Updates to handle problematic waterbody data

Two major updates:

Fix issue of duplicate integer IDs between some waterbodies and stream segments. We now add a large number to any duplicate waterbody ID initially, then revert back to the original ID before writing output files.
Some waterbodies have flowpaths that physically lie within them, but are not referenced to the waterbody ID. This causes issues when collapsing segment IDs into a single waterbody ID in our connections dictionary (multiple "downstream" IDs which violates the DAG). These waterbodies are simply "dropped" as waterbodies, meaning the underlying segments are used for MC routing.

Additions

AbstractRouting.py

Updates to finding outlet IDs of waterbodies. The old method became an issue for a waterbody in Florida that directly flows into the ocean.

HYFeaturesNetwork.py

Update to bandaid() function to simply drop problematic waterbody IDs.
Change fix for duplicate IDs. Old method added a large value to flowpath IDs, now it adds to waterbody IDs.
Saves the duplicate_ids crosswalk dictionary to revert changes before producing output.

output.py

main.py

Successfully ran a dummy (unrealistic forcing inputs) CONUS run with waterbodies enabled.
Verified output files contain original IDs.

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