SIP350 Update carbon accounting + plant mortality

[Alomir]

Summary

• What: Revamp handling of the C pseudo-storage pool
• Motivation: Current handling is broken.

NOTE: THIS REPLACES #353

How was this change tested?

• Existing unit tests updated
• New unit tests added to cover new functionality
• Smoke tests run and updated; diff results below

smoke_check.txt

Related issues

• Fixes Revamp biomass N handling #350

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)

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[Alomir]

@copilot please open a PR to update the unit tests in tests/sipnet to cover these changes. Create new similar tests if needed.

[Copilot]

@Alomir I've opened a new pull request, #360, to work on those changes. Once the pull request is ready, I'll request review from you.

[Copilot]

Pull request overview

This PR revamps SIPNET’s carbon “accounting/buffer” handling (renaming plantWoodCStorageDelta → plantCAccountingDelta), adds a plant mortality/reemergence tracker with event output, updates restart/debug-log serialization to include the new tracker and event fields, and refreshes the Python viewer tools plus unit/smoke coverage accordingly.

Changes:

• Rework biomass C flux calculations to account for negative mean NPP and to use the carbon accounting delta consistently; add plant mortality detection and plantdeath event output.
• Extend restart/debug logging schemas (survival tracker + expanded event trackers) and update unit tests/new modeling tests.
• Refactor sipnet-view / sipnet-debug-view tooling (shared arg parser, plot controls, toolbar hover display), plus smoke harness updates (optional debug-log runs).

Reviewed changes

Copilot reviewed 30 out of 34 changed files in this pull request and generated 7 comments.

Show a summary per file

File	Description
tools/sipnet_view.py	Adds configurable viewer window title; switches to shared default CLI parser.
tools/sipnet_view_common.py	Adds shared CLI parser helper, plot display controls, and custom toolbar hover reporting.
tools/sipnet_debug_view.py	Adds configurable window title; uses shared default CLI parser; minor perf copy before sorting/merging.
tests/smoke/russell_3/events.out	Updates expected computed event outputs after new accounting/mortality behavior.
tests/smoke/russell_2/events.out	Updates expected computed event outputs after new accounting/mortality behavior.
tests/smoke/russell_1/sipnet.config	Updates recorded “Final config” timestamp from smoke run.
tests/smoke/russell_1/events.out	Updates expected computed event outputs after new accounting/mortality behavior.
tests/smoke/run_smoke.sh	Adds optional debug-log generation mode for smoke runs.
tests/sipnet/test_sipnet_infrastructure/testDebugLogFiles.c	Updates debug-log header expectations; adds init/cleanup to avoid leaving modified files behind.
tests/sipnet/test_restart_infrastructure/mock_state.c	Updates restart schema drift mocking to use renamed accounting field.
tests/sipnet/test_modeling/testPlantMortality.c	New unit test suite for mortality + pool transfers (with/without litter and nitrogen).
tests/sipnet/test_modeling/testNitrogenCycle.c	Adds focused unit test for the new incremental N resorption flux helper.
tests/sipnet/test_modeling/testFluxCalculations.c	New unit tests for wood/leaf/root flux calculation behavior under positive/negative NPP.
tests/sipnet/test_modeling/Makefile	Adds new modeling test files to the test build.
tests/sipnet/test_events_types/testEventHarvest.c	Updates event test setup to use renamed carbon accounting delta field.
src/sipnet/state.h	Renames carbon accounting pool; introduces PlantSurvivalTracker; expands EventTrackers.
src/sipnet/state.c	Adds global plantSurvivalTracker and reorders globals.
src/sipnet/sipnet.c	Refactors flux calculations; adds plant survival init + mortality checks; updates trackers behavior.
src/sipnet/restart.c	Updates restart schema layout + read/write logic to include survival tracker + expanded event trackers.
src/sipnet/nitrogen.h	Renames N demand function; adds N resorption helper API; clarifies docs.
src/sipnet/nitrogen.c	Implements renamed demand function and new updateNResorptionFlux() helper.
src/sipnet/limitations.c	Updates nitrogen limitation logic to use renamed demand function.
src/sipnet/events.h	Adds PLANTDEATH event type; expands EventTrackers; fixes typo in comment.
src/sipnet/events.c	Adds plantdeath type-string support; tracks harvest fractions; extends event printing.
src/sipnet/depeffects.c	Adds missing include needed after header reshuffle.
src/sipnet/debug_log.c	Updates debug field lists and outputs to include survival tracker state.
src/sipnet/balance.c	Updates carbon accounting pool name and improves warning numeric formatting.
Makefile	Adds smokedebug target and debug-log cleanup in cleanall.
docs/CHANGELOG.md	Documents new debug viewer, plant mortality event output, and carbon accounting changes.
.github/copilot_instructions.md	Adds changelog formatting guidelines for Copilot-generated text.

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