Address PR #248 review feedback: document wood carbon storage pool

[Copilot]

• Revert code changes (balance.c and state.h) per reviewer request
• Remove Mass Balance Checks section from model-structure.md (not required)
• Update Wood Carbon section in model-structure.md to describe explicit storage pool
• Add plantWoodCStorageDelta documentation to parameters.md
• Remove accidentally committed test output files
• Update .gitignore to exclude generated test outputs
• Fix line 137 in model-structure.md: remove "accurate" and code parameter name
• Run tests - all pass

Summary

Per review feedback, this PR now focuses only on documentation updates:

Documentation Changes

model-structure.md:

• Updated Wood Carbon section to describe that the storage pool is now explicitly tracked as $C_{\text{wood,storage}}$ (starting in v2.1)
• Added equation for total wood carbon: $C_{\text{wood,total}} = C_{\text{wood}} + C_{\text{wood,storage}}$
• Explained storage represents lag between NPP input and allocation output due to 5-day averaging
• Removed "accurate" qualifier (implied)
• Removed code parameter name from documentation (kept only mathematical notation)

parameters.md:

• Added entry for $C_{\text{wood,storage}}$ (plantWoodCStorageDelta) in state variables table
• Documented that it tracks NPP/allocation lag, is initialized to 0, and can be negative
• Clarified total wood C is sum of structural wood + storage

CHANGELOG.md:

• Entries remain for carbon balance check feature (SIP208, SIP209 Add carbon balance check #248)

Code Changes

• All code changes reverted per reviewer request (balance.c and state.h restored to original state)

Test Files

• Removed accidentally committed test output files (events.out)
• Updated .gitignore to properly exclude generated test outputs while keeping expected outputs

All tests pass.

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[dlebauer]

Needs to include description of the storage pool.

Needs to update parameters.

Code should not be updated.

[dlebauer]

Not required for model structure doc

[Copilot]

Removed in 1a071ee. The Mass Balance Checks section has been removed from model-structure.md.

[Copilot]

Needs to include description of the storage pool.

Needs to update parameters. ...

Completed in 1a071ee:

✅ Storage pool description added: Updated Wood Carbon section in model-structure.md to document plantWoodCStorageDelta as explicit storage pool tracking NPP/allocation lag
✅ Parameters updated: Added entry in parameters.md for $C_{\text{wood,storage}}$ with full description
✅ Code reverted: All code changes in balance.c and state.h have been reverted to original state

The documentation now properly describes the explicit storage pool implementation without making code changes.

[dlebauer]

Why are doc updates accompanied by updates to test files?

[dlebauer]

Remove "accurate". It is implied. Don't add parameter name used in code here, that isn't done elsewhere in this file. The mapping between mathematical symbols and parameter names are in parameters.md. Does the document have sufficient description of the dynamics added in the PR that this PR will be merged into? If needed, make sure it is consistent with the document as a whole and the current state of the code.

[Copilot]

Fixed in 305769d:

• Removed "accurate" qualifier
• Removed code parameter name (plantWoodCStorageDelta)
• Line now reads: "Starting in SIPNET v2.1, to support mass balance tracking, this storage is explicitly tracked as a separate pool called $C_{\text{wood,storage}}$."

The mathematical notation $C_{\text{wood,storage}}$ is mapped to the code name in parameters.md as requested.

[Copilot]

Why are doc updates accompanied by updates to test files?

The test output files (events.out) were accidentally committed when tests were run during development. Removed in 305769d. Also updated .gitignore to properly exclude generated test outputs (events.out, sipnet.out, sipnet.config) while preserving expected output files.

[Alomir]

Please remove the "In code:" reference here, we don't do that for other params