resolve linker errors

.gitignore

@@ -2,6 +2,7 @@
 *.slo
 *.lo
 *.o
+.idea/*
 
 # Compiled Dynamic libraries
 *.so
@@ -185,4 +186,4 @@ $RECYCLE.BIN/
 .vscode
 
 # Doxygen Folder
-Doxygen
+Doxygen

CLAUDE.md

@@ -0,0 +1,144 @@
+# CLAUDE.md
+
+This file provides guidance to Claude Code (claude.ai/code) when working with code in this repository.
+
+## Overview
+
+EPANET-MSX is a multi-species extension to the EPANET hydraulic analysis engine for modeling chemical species fate and transport in water distribution systems. The codebase is structured as a modular C/C++ project with three main components designed to provide both backwards compatibility and modern toolkit functionality.
+
+## Architecture
+
+The project is organized into three interdependent modules:
+
+1. **MSX Core** (`MSX Core/`) - Core mathematical and chemical reaction engine
+   - Contains all simulation algorithms and chemical reaction code
+   - Provides modern toolkit API via `coretoolkit.h` 
+   - Has no external dependencies (self-contained)
+   - Key files: `msxtoolkit.c`, `msxchem.c`, `msxqual.c`, `msxcompiler.c`
+
+2. **Legacy DLL** (`Legacy DLL/`) - Backwards compatibility layer
+   - Parses traditional EPANET (.inp) and MSX (.msx) input files
+   - Provides legacy API functions for existing applications
+   - Depends on MSX Core and external EPANET library
+   - Key files: `legacytoolkit.c`, `msxinp.c`, `msxfile.c`, `msxrpt.c`
+
+3. **CLI** (`CLI/`) - Command-line interface
+   - Provides executable interface using both Core and Legacy APIs
+   - Depends on both MSX Core and Legacy DLL
+   - Main entry point: `CLI/run/msxmain.c`
+
+4. **Example API** (`example-api/`) - Example implementations
+   - Demonstrates usage of both legacy and modern APIs
+   - Optional module for building examples
+
+## Build System
+
+The project uses CMake with a specific build order due to dependencies:
+
+### Docker Build (Recommended)
+```bash
+docker run --rm -it -v "$PWD":/epanet-msx -w /epanet-msx cmake-dev bash
+./docker_embedded_build.sh
+```
+
+### Quick Build (Local)
+```bash
+./build.sh
+```
+
+### Manual Build Process
+Must be built in this exact order:
+
+1. **MSX Core** (no dependencies):
+```bash
+cd "MSX Core"
+mkdir build && cd build
+cmake ..
+cmake --build . --config Release
+```
+
+2. **Legacy DLL** (depends on MSX Core + external EPANET):
+```bash
+cd "Legacy DLL"  
+mkdir build && cd build
+cmake ..
+cmake --build . --config Release
+```
+
+3. **Example API** (optional):
+```bash
+cd example-api
+mkdir build && cd build
+cmake ..
+cmake --build . --config Release
+```
+
+4. **CLI** (depends on all above):
+```bash
+cd CLI
+mkdir build && cd build
+cmake ..
+cmake --build . --config Release
+```
+
+### Important Build Notes
+- EPANET repository must be built in the same parent directory as epanet-msx
+- The build script automatically copies required DLLs to the CLI build directory
+- Required DLLs for CLI: `msxcore.dll`, `legacymsx.dll`, `epanet2.dll`, `examples.dll`
+
+## API Usage Patterns
+
+### Modern Core API (MSXproject-based)
+```c
+MSXproject MSX;
+MSX_open(&MSX);
+// Configure network, species, chemistry
+MSX_init(MSX);
+// Set hydraulics
+while (timeLeft >= 0) {
+    MSXstep(MSX, &time, &timeleft);
+}
+MSX_close(MSX);
+```
+
+### Legacy API (Global state)
+```c
+MSXopen();
+// Configure via file parsing
+MSXinit();
+while (timeLeft >= 0) {
+    MSXstep(&time, &timeleft);
+}
+MSXclose();
+```
+
+## Key Implementation Details
+
+- **Chemical Solver**: Uses numerical methods (RK5, ROS2, Newton) for reaction kinetics
+- **Data Structures**: Hash tables for object lookup, memory pools for allocation
+- **Cross-platform**: Windows/Linux compatible with appropriate DLL/shared library handling
+- **Thread Safety**: Not thread-safe - single instance per process
+- **Error Handling**: Integer return codes with `MSXgeterror()` for message retrieval
+
+## Testing
+
+The repository includes example networks and test cases in `example-api/legacy-examples/`:
+- `Batch-NH2Cl/` - Batch reactor chloramine decay
+- `Net2-CL2/` - Network chlorine simulation  
+- `Net3-NH2Cl/` - Large network chloramine modeling
+- `As5Adsorb/` - Arsenic adsorption modeling
+
+## Development Workflow
+
+1. Make changes to appropriate module (Core, Legacy DLL, or CLI)
+2. Build dependencies first, then target module
+3. Test with provided examples
+4. For new features, prefer extending Core API over Legacy API
+5. Maintain backwards compatibility in Legacy DLL
+
+## File Extensions and Formats
+
+- `.inp` - EPANET hydraulic network input files
+- `.msx` - MSX chemical species and reaction input files  
+- `.rpt` - Text report output files
+- `.out` - Binary results output files

Legacy DLL/CMakeLists.txt

@@ -55,7 +55,7 @@ IF(MSVC)
   target_link_libraries(legacymsx ${EPANET_LIB} ${MSXCORE_LIB} OpenMP::OpenMP_C)
 ELSE(TRUE)
   add_library(legacymsx SHARED ${MSX_SOURCES})
-  target_link_libraries(legacymsx ${EPANET_LIB} ${MSXCORE_LIB} OpenMP::OpenMP_C)
+  target_link_libraries(legacymsx ${EPANET_LIB} ${MSXCORE_LIB} OpenMP::OpenMP_C m)
 ENDIF(MSVC)
 
 target_include_directories(legacymsx PUBLIC ${PROJECT_SOURCE_DIR}/include)

MSX Core/src/msxfuncs.c

@@ -34,6 +34,14 @@ HMODULE hDLL;
 
 #include "msxfuncs.h"
 
+// Define the chemistry function pointers
+MSXGETRATES    MSXgetPipeRates = NULL;
+MSXGETRATES    MSXgetTankRates = NULL;
+MSXGETEQUIL    MSXgetPipeEquil = NULL;
+MSXGETEQUIL    MSXgetTankEquil = NULL;
+MSXGETFORMULAS MSXgetPipeFormulas = NULL;
+MSXGETFORMULAS MSXgetTankFormulas = NULL;
+
 //=============================================================================
 
 int MSXfuncs_load(char * libName)

MSX Core/src/msxfuncs.h

@@ -18,12 +18,12 @@ typedef void (*MSXGETEQUIL)(double *, double *, double * , double *, double *);
 typedef void (*MSXGETFORMULAS)(double *, double *, double *, double *);
 
 // Declare each chemistry function
-MSXGETRATES    MSXgetPipeRates;
-MSXGETRATES    MSXgetTankRates;
-MSXGETEQUIL    MSXgetPipeEquil;
-MSXGETEQUIL    MSXgetTankEquil;
-MSXGETFORMULAS MSXgetPipeFormulas;
-MSXGETFORMULAS MSXgetTankFormulas;
+extern MSXGETRATES    MSXgetPipeRates;
+extern MSXGETRATES    MSXgetTankRates;
+extern MSXGETEQUIL    MSXgetPipeEquil;
+extern MSXGETEQUIL    MSXgetTankEquil;
+extern MSXGETFORMULAS MSXgetPipeFormulas;
+extern MSXGETFORMULAS MSXgetTankFormulas;
 
 // Functions that load and free the chemistry functions
 int  MSXfuncs_load(char *);

docker_embedded_build.sh

@@ -0,0 +1,9 @@
+#!/usr/bin/env bash
+
+cd 'MSX Core' || exit
+
+mkdir -p build
+cd build || exit
+cmake .. || exit
+cmake --build . --config Release
+