SIP333 docs (#335)

* update model structure b/c not all source is in sipnet.c

* added check limitations to code-structure doc

Author: dlebauer

docs/developer-guide/code-structure.md

@@ -8,14 +8,15 @@ This guide documents how state is advanced each timestep and the conventions tha
 - Zero all `fluxes.*` and `fluxes.event*`.
 
 2) Compute fluxes (pure calculations)
-- `calculateFluxes()` computes photosynthesis, respiration, water/snow, etc.
 - `processEvents()` converts scheduled/instant events to `fluxes.event*` deltas (no pool mutation).
--  No function in this phase mutates `envi.*` or `trackers.*`.
-
+- `calculateFluxes()` computes photosynthesis, respiration, water/snow, etc.
+- `checkLimitations()` may adjust already-computed fluxes when a flux is resource limited.
+- No function in this phase mutates `envi.*` or `trackers.*`.
 
 3) Apply pool updates (single place)
 - `updateMainPools()` updates leafC, woodC, soil water and snow pools
 - `updatePoolsForSoil()` updates soil carbon pools
+- `updateNitrogenPools()` updates mineral, soil organic, and litter nitrogen pools.
 - `updatePoolsForEvents()` updates pools for fluxes from events
 - The above functions are the only code that changes `envi.*`.
 - For each pool P: ΔP = ((sum of rate fluxes to P) + (sum of event fluxes to P)) * climate.length

docs/model-structure.md

@@ -24,7 +24,7 @@ This document provides an overview of the SIPNET model’s structure. It was wri
 - Focus on features currently in regular use.
 
 There are multiple ways to configure the model structure, and not all model structures or components are listed.
-Implementation in source code (sipnet.c) is annotated with references to specific publications.
+Implementation in source code is annotated with references to specific publications.
 
 #### Notes on notation:
 
@@ -1174,7 +1174,7 @@ nitrogen (calculated from the leaf C:N ratio) is also transferred to the litter
 **Event parameters:**
 
 | Parameter | Value                | Description       |
-|-----------|----------------------|-------------------|
+| --------- | -------------------- | ----------------- |
 | Year      | integer              | Year              |
 | Day       | integer              | Day of year       |
 | Type      | `leafon` / `leafoff` | The type of event |