SIP400 Address harvest and leaf off issues

[Alomir]

Summary

• What: Fix discovered issues with harvest and leaf-on mechanics
• Motivation: Non-negative pool sizes and mass imbalances occur without these changes

How was this change tested?

• Current tests all pass (after updates for slightly altered flow)
• Extensive new test passes
• Smoke tests pass without any modifications to sipnet.out files (one minor changes to russell_2/events.out)

Related issues

• Fixes Address harvest and leaf off mass conservation issues #400
• Fixes Consider leaf-off litter and event fluxes in negative-growth limitation check #372

Checklist

• Related issues are listed above. PRs without an approved, related issue may not get reviewed.
• PR title has the issue number in it ("[#] <concise description of proposed change>")
• Tests added/updated for new features (if applicable)
• Documentation updated (if applicable)
• docs/CHANGELOG.md updated with noteworthy changes
• Code formatted with clang-format (run git clang-format if needed)

[dlebauer]

When I asked Chad to "just make it work, please" (referring to the entire MAGic pipeline) Chad did this (among other things):

master...dlebauer:sipnet:fix/zero-carbon-nitrogen-transfer

And now that this is up he said:

In calcNPoolFluxes(), there are three remaining cases where a zero C flux can be divided by an undefined C:N ratio when the corresponding C pool is empty: rLitter / litterCN, rSoil / soilCN, and litterToSoil / litterCN. This produces NaN nitrogen fluxes.

Could we guard each calculation so that a zero carbon flux carries zero nitrogen? I have a small patch and regression test for this and can update them to preserve the new getLeafLitterFlux() logic in this PR.

[Alomir]

@dlebauer I like that! Go Chad!

[Alomir]

I'm going to go ahead and make a PR for Chad's changes, rather than make this one bigger

[Alomir]

Moving to ready for review - I suspect copilot will point out some doc updates I missed.

[Copilot]

Copilot review overview

🟡 Changes recommended

Harvest deltas remain absent from pool look-ahead checks, and leaf-off logs can report pre-limitation values.

Review effort: Balanced
Findings: 2

Open (2)

• Log finalized leaf-off carbon and nitrogen fluxes · New
• Include leaf event deltas in nonnegative stock look-ahead · New

What changed in this PR

Fixes harvest and leaf-off mass conservation by restructuring event processing, adding harvest termination handling, and expanding regression coverage.

Changes:

• Splits event processing into carbon and nitrogen passes.
• Tracks harvest routing and leaf-off fluxes more precisely.
• Adds comprehensive harvest, balance, restart, and event-output tests.

File	Description
src/​common/​exitCodes.h	Adds allocation-failure exit code.
src/​common/​util.c	Implements dynamic strings.
src/​common/​util.h	Declares dynamic-string API.
src/​sipnet/​balance.c	Improves imbalance diagnostics.
src/​sipnet/​debug_log.c	Logs new flux and event fields.
src/​sipnet/​events.c	Splits event passes and revises harvest handling.
src/​sipnet/​events.h	Adds event logs and harvest trackers.
src/​sipnet/​limitations.c	Extends negative-pool limitation logic.
src/​sipnet/​nitrogen.c	Separates leaf-off nitrogen effects.
src/​sipnet/​nitrogen.h	Exposes leaf-off nitrogen helper.
src/​sipnet/​restart.c	Serializes expanded event trackers.
src/​sipnet/​sipnet.c	Integrates event passes and mortality correction.
src/​sipnet/​state.c	Adds combined leaf-litter accessor.
src/​sipnet/​state.h	Adds new event and leaf-off fluxes.
tests/​sipnet/​test_events_infrastructure/​events_output_header.out	Updates expected event output.
tests/​sipnet/​test_events_infrastructure/​events_output_no_header.out	Updates headerless event output.
tests/​sipnet/​test_events_types/​testEventHarvest.c	Tests accounting-carbon harvests.
tests/​sipnet/​test_modeling/​Makefile	Registers the harvest regression suite.
tests/​sipnet/​test_modeling/​termination.clim	Adds regression climate fixture.
tests/​sipnet/​test_modeling/​termination.param	Adds regression parameter fixture.
tests/​sipnet/​test_modeling/​testCompleteHarvest.c	Adds comprehensive harvest regressions.
tests/​sipnet/​test_modeling/​testNitrogenCycle.c	Updates event/N-cycle sequencing tests.
tests/​sipnet/​test_modeling/​testPlantMortality.c	Uses expanded harvest trackers.
tests/​sipnet/​test_sipnet_infrastructure/​testDebugLogFiles.c	Validates expanded debug output.
tests/​smoke/​russell_2/​events.out	Updates smoke-test field ordering.
tests/​utils/​helpers.c	Updates test event processing flow.
docs/​CHANGELOG.md	Documents harvest and leaf-off fixes.

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[Alomir]

Yeah, fine, I was clearly ignoring this as these outputs are really just for debugging. However, we're in a decent place for doing this in a centralized/extendable way, so why not...

[Alomir]

This one is harder, as I don't think this is the best place to handle eventLeafC overdraws.

Hmm, maybe as a step between leaf-off litter and transfer to woodC... that might work. This will mess up the test, so more work there.