AntaresSimulatorTeam · nikolaredstork · Jun 30, 2026 · Jun 30, 2026 · Jun 30, 2026 · Jul 1, 2026
diff --git a/AGENTS.md b/AGENTS.md
@@ -50,11 +50,11 @@ Full reference documentation lives in `doc/`. Read the relevant file before edit
 
 | Topic | Reference |
 |-------|-----------|
-| GEMS study file types and domains (model libraries, system, timeseries, solver, business views) | [`doc/overview/file-structure.md`](doc/overview/file-structure.md) |
-| Library file structure (port-types, models, parameters, variables, constraints) | [`doc/user-guide/file-structure/library.md`](doc/user-guide/file-structure/library.md) |
+| GEMS study file types and domains (model libraries, system, timeseries, solver, views) | [`doc/overview/file-structure.md`](doc/overview/file-structure.md) |
+| Library file structure (port-types, models, parameters, variables, constraints) | [`doc/user-guide/input-files/library.md`](doc/user-guide/input-files/library.md) |
 | Mathematical expression syntax (operators, time indexing, aggregation, linearity) | [`doc/user-guide/mathematical-syntax.md`](doc/user-guide/mathematical-syntax.md) |
-| Study folder layout (system.yml, data-series/, model-libraries/, optim-config.yml, parameters.yml) | [`doc/user-guide/file-structure/overview.md`](doc/user-guide/file-structure/overview.md) |
-| System file (components, connections, parameter assignment) | [`doc/user-guide/file-structure/system.md`](doc/user-guide/file-structure/system.md) |
+| Study folder layout (system.yml, data-series/, model-libraries/, optim-config.yml, parameters.yml) | [`doc/user-guide/input-files/overview.md`](doc/user-guide/input-files/overview.md) |
+| System file (components, connections, parameter assignment) | [`doc/user-guide/input-files/system.md`](doc/user-guide/input-files/system.md) |
 
 ---
 

diff --git a/doc/getting-started/installation/modeler-installation.md b/doc/getting-started/installation/modeler-installation.md
@@ -141,7 +141,7 @@ Replace `<path-to-study>` with the path to your Antares study directory.
 
 The complete installation, documentation is available on the [official documentation website](https://antares-simulator.readthedocs.io/en/latest/user-guide/02-install/).
 
-In addition, Antares Modeler requires inside, the study folder, a `parameters.yml` file to run a GEMS study , and the process for creating this file is detailed in [this section](../../user-guide/file-structure/solver-optimization.md). Unlike the GemsPy interpreter, Modeler depends on this configuration file.
+In addition, Antares Modeler requires inside, the study folder, a `parameters.yml` file to run a GEMS study , and the process for creating this file is detailed in [this section](../../user-guide/input-files/solver-optimization.md). Unlike the GemsPy interpreter, Modeler depends on this configuration file.
 
 ## Additional Resources
 

diff --git a/doc/getting-started/quick-start/unit-commitment.md b/doc/getting-started/quick-start/unit-commitment.md
@@ -124,7 +124,7 @@ The mathematical modelling used for this study case is inspired from Antares Sim
 
 ### Library File
 
-The library file [**antares_legacy_models.yml**](https://github.com/AntaresSimulatorTeam/GEMS/blob/main/libraries/antares_legacy_models.yml) defines the main component [models](../../user-guide/file-structure/library.md#models) used in this example:
+The library file [**antares_legacy_models.yml**](https://github.com/AntaresSimulatorTeam/GEMS/blob/main/libraries/antares_legacy_models.yml) defines the main component [models](../../user-guide/input-files/library.md#models) used in this example:
 
 - **bus**: Central node with power balance constraint, spillage, and unsupplied energy variables.
 - **load**: Consumes power (negative flow into the bus).

diff --git a/doc/home/core-concepts.md b/doc/home/core-concepts.md
@@ -31,11 +31,11 @@ This language **differs from traditional optimization languages** in several way
 
 <h3> Library </h3>
 
-A YAML file defining abstract objects called <a href="../user-guide/file-structure/library.md#models">models</a>, which describe the mathematical formulation of a category of energy system element.
+A YAML file defining abstract objects called <a href="../user-guide/input-files/library.md#models">models</a>, which describe the mathematical formulation of a category of energy system element.
 
 <br>
 <br>
-For more details, see the <a href="../user-guide/file-structure/library.md"><b>Library</b></a> page of the user guide.
+For more details, see the <a href="../user-guide/input-files/library.md"><b>Library</b></a> page of the user guide.
 
 ```yaml
 library:
@@ -94,7 +94,7 @@ library:
 A YAML file describing the concrete energy system to be simulated. It instantiates components from models provided by the libraries, assigns parameter values, and defines the connections between components.
 
 <br>
-For more details, see the <a href="../user-guide/file-structure/system.md"><b>System</b></a> page of the user guide.
+For more details, see the <a href="../user-guide/input-files/system.md"><b>System</b></a> page of the user guide.
 
 ```yaml
 system:

diff --git a/doc/index.md b/doc/index.md
@@ -43,7 +43,7 @@ The following **interpreters** can be used to run Gems modelling language :
 **Converters** are available to translate existing studies into the GEMS modelling language:
 
 - [Antares Legacy Models to GEMS Converter](https://github.com/AntaresSimulatorTeam/AntaresLegacyModels-to-GEMS-Converter) : a Python package that enables the migration of Antares Legacy Models to GEMS.
-- [PyPSA to Gems Converter](https://github.com/AntaresSimulatorTeam/PyPSA-to-GEMS-Converter), a stand-alone Python package to export PyPSA [Networks](https://docs.pypsa.org/v1.0.2/user-guide/design/#network-object) as [GEMS system](./user-guide/file-structure/system.md). This converter supports [PyPSA two-stage stochastic optimization problems](https://docs.pypsa.org/v1.0.2/user-guide/optimization/stochastic/): such problems can be addressed by GEMS [interpreters](./overview/architecture.md) and solved with [Antares Xpansion's Benders decomposition algorithm](https://antares-xpansion.readthedocs.io/en/stable/).
+- [PyPSA to Gems Converter](https://github.com/AntaresSimulatorTeam/PyPSA-to-GEMS-Converter), a stand-alone Python package to export PyPSA [Networks](https://docs.pypsa.org/v1.0.2/user-guide/design/#network-object) as [GEMS system](./user-guide/input-files/system.md). This converter supports [PyPSA two-stage stochastic optimization problems](https://docs.pypsa.org/v1.0.2/user-guide/optimization/stochastic/): such problems can be addressed by GEMS [interpreters](./overview/architecture.md) and solved with [Antares Xpansion's Benders decomposition algorithm](https://antares-xpansion.readthedocs.io/en/stable/).
 
 
 ## Documentation Highlights

diff --git a/doc/interoperability/hybrid/hybrid-connections.md b/doc/interoperability/hybrid/hybrid-connections.md
@@ -12,9 +12,9 @@ In practical terms, connecting a GEMS **Generator** component to an Antares Lega
 
 The following steps describe how to **link the GEMS part of the study to the Legacy part**:
 
-## Abstract definition of the area-connection field type (in the [library](../../user-guide/file-structure/library.md) file)
+## Abstract definition of the area-connection field type (in the [library](../../user-guide/input-files/library.md) file)
 
-In order to successfully inject a GEMS component's port into an Antares Legacy Area, the port's type must declare which field will contribute to the optimization problem. This is configured in the [library](../../user-guide/file-structure/library.md) of the component's model (e.g. a file `model-libraries/library.yml`). 
+In order to successfully inject a GEMS component's port into an Antares Legacy Area, the port's type must declare which field will contribute to the optimization problem. This is configured in the [library](../../user-guide/input-files/library.md) of the component's model (e.g. a file `model-libraries/library.yml`). 
 
 The `area-connection` section is optional in general, but becomes mandatory when the port type is intended to be used in a **hybrid study**. It can accept 3 types of fields `injection-to-balance`, `spillage-bound` and `unsupplied-energy-bound` :
 
@@ -93,7 +93,7 @@ When connecting a component to an area, you must respect conventions on the sign
         ```
 
 
-## Definition of the area-connections (in the [system](../../user-guide/file-structure/system.md) file)
+## Definition of the area-connections (in the [system](../../user-guide/input-files/system.md) file)
 
 The `area-connections` section of the system file is used to declare each connection between a GEMS component and an Antares Legacy Area.
 

diff --git a/doc/interoperability/pypsa-to-gems-converter/how-the-converter-works.md b/doc/interoperability/pypsa-to-gems-converter/how-the-converter-works.md
@@ -6,7 +6,7 @@
 
 # How the Converter Works
 
-The PyPSA to GEMS Converter transforms [PyPSA Network](https://docs.pypsa.org/latest/api/networks/network/) into a [GEMS study folder](https://gems-energy.readthedocs.io/en/latest/user-guide/file-structure/overview/), through the following steps.
+The PyPSA to GEMS Converter transforms [PyPSA Network](https://docs.pypsa.org/latest/api/networks/network/) into a [GEMS study folder](https://gems-energy.readthedocs.io/en/latest/user-guide/input-files/overview/), through the following steps.
 
 ## 1. Input Validation and Preprocessing
 

diff --git a/doc/interoperability/pypsa-to-gems-converter/overview.md b/doc/interoperability/pypsa-to-gems-converter/overview.md
@@ -14,7 +14,7 @@ The [PyPSA-to-GEMS](https://github.com/AntaresSimulatorTeam/PyPSA-to-GEMS-Conver
 is an open-source & standalone python package that enables the conversion of studies 
 conducted in PyPSA into the GEMS format: it exports a 
 [PyPSA Network](https://docs.pypsa.org/latest/api/networks/network.md) as a 
-[GEMS](https://gems-energy.readthedocs.io/en/latest/user-guide/file-structure/overview.md) folder.
+[GEMS](https://gems-energy.readthedocs.io/en/latest/user-guide/input-files/overview.md) folder.
 
 This converter is based on the representation of the PyPSA models of components as a GEMS library of models: [pypsa_models.yml](https://github.com/AntaresSimulatorTeam/GEMS/blob/main/libraries/pypsa_models.yml).
 

diff --git a/doc/overview/file-structure.md b/doc/overview/file-structure.md
@@ -20,13 +20,13 @@ The different types of files describing a GEMS study case are:
 
 | **Type of File**   | **Domain**  | **File**        | **Description & Role**  |
 |---------------------|-------------|-----------------|-------------------------|
-| **[Model Libraries](../user-guide/file-structure/library.md)** | <span style="display:inline-block; width:12px; height:12px; background-color:#17A2B8; border-radius:50%; margin-right:5px;"></span>Abstract modelling | YAML (e.g., `basic-models-library.yml`, `antares-models-library.yml`)  |**Defines Models:** Abstract representations of system components to be simulated. **Models are defined in a library file** and specifies its ports, parameters, and internal behavior.These definitions can also include optional constraint and objective contributions used in simulation.|
-| **[Taxonomy](../user-guide/file-structure/taxonomy.md)**| <span style="display:inline-block; width:12px; height:12px; background-color:#17A2B8; border-radius:50%; margin-right:5px;"></span>Abstract modelling| YAML (e.g., `taxonomy.yml`)| **Model Structure & Categories:** Specifies mandatory parameters, variables, ports, or extra outputs per category. Useful for structuring the UI (user interface) and simulation outputs.|
-| **[System](../user-guide/file-structure/system.md)**  | <span style="display:inline-block; width:12px; height:12px; background-color:#D63384; border-radius:50%; margin-right:5px;"></span>System  | YAML  (`system.yml`) | **Defines Components:** Numerical instantiation of models, linking to model IDs (e.g., `example_library_id.example_model_id`). Specifies parameter values and connections between components via ports, forming the system graph.|
-| **[Timeseries](../user-guide/file-structure/data-series.md)**  | <span style="display:inline-block; width:12px; height:12px; background-color:#D63384; border-radius:50%; margin-right:5px;"></span>System  | Dataseries (e.g., `wind_generation.csv`, `solar_generation.csv`)  | **Time-dependent Data:** Numerical data for parameters varying by time and scenario. Stored as `.csv` or `.tsv` files, typically in a data-series folder.|
+| **[Model Libraries](../user-guide/input-files/library.md)** | <span style="display:inline-block; width:12px; height:12px; background-color:#17A2B8; border-radius:50%; margin-right:5px;"></span>Abstract modelling | YAML (e.g., `basic-models-library.yml`, `antares-models-library.yml`)  |**Defines Models:** Abstract representations of system components to be simulated. **Models are defined in a library file** and specifies its ports, parameters, and internal behavior.These definitions can also include optional constraint and objective contributions used in simulation.|
+| **[Taxonomy](../user-guide/input-files/taxonomy.md)**| <span style="display:inline-block; width:12px; height:12px; background-color:#17A2B8; border-radius:50%; margin-right:5px;"></span>Abstract modelling| YAML (e.g., `taxonomy.yml`)| **Model Structure & Categories:** Specifies mandatory parameters, variables, ports, or extra outputs per category. Useful for structuring the UI (user interface) and simulation outputs.|
+| **[System](../user-guide/input-files/system.md)**  | <span style="display:inline-block; width:12px; height:12px; background-color:#D63384; border-radius:50%; margin-right:5px;"></span>System  | YAML  (`system.yml`) | **Defines Components:** Numerical instantiation of models, linking to model IDs (e.g., `example_library_id.example_model_id`). Specifies parameter values and connections between components via ports, forming the system graph.|
+| **[Timeseries](../user-guide/input-files/data-series.md)**  | <span style="display:inline-block; width:12px; height:12px; background-color:#D63384; border-radius:50%; margin-right:5px;"></span>System  | Dataseries (e.g., `wind_generation.csv`, `solar_generation.csv`)  | **Time-dependent Data:** Numerical data for parameters varying by time and scenario. Stored as `.csv` or `.tsv` files, typically in a data-series folder.|
 | **Solution Workflow**| <span style="display:inline-block; width:12px; height:12px; background-color:#F8A055; border-radius:50%; margin-right:5px;"></span>Solution Workflow| YAML (`optim-config.yml`)| **Workflow Definition:** Describes calculation block processing (sequential, parallel, Xpansion frontale, Benders decomposition) and master problem constraints, especially for investment variables.|
-|**[Optimization Parameters](../user-guide/file-structure/solver-optimization.md)**| <span style="display:inline-block; width:12px; height:12px; background-color:#F8A055; border-radius:50%; margin-right:5px;"></span>Solution Workflow| YAML (`parameters.yml`)| **Solver & Configuration Settings:** Contains solver parameters and configuration required for running Modeler.|
-| **[Business Views Configurations](../user-guide/file-structure/business-view-configuration.md)**| <span style="display:inline-block; width:12px; height:12px; background-color:#8B5FB5; border-radius:50%; margin-right:5px;"></span>Business Intelligence| YAML (e.g., `business-view-def.yml`, `business-metric.yml`) | **Business Metrics Logic:** Calculates business metrics from simulation results in two phases: Step 1 (component scope, complex arithmetic), Step 2 (global scope, aggregation/filtering).|
+|**[Optimization Parameters](../user-guide/input-files/solver-optimization.md)**| <span style="display:inline-block; width:12px; height:12px; background-color:#F8A055; border-radius:50%; margin-right:5px;"></span>Solution Workflow| YAML (`parameters.yml`)| **Solver & Configuration Settings:** Contains solver parameters and configuration required for running Modeler.|
+| **[Business Views Configurations](../user-guide/input-files/view-configuration.md)**| <span style="display:inline-block; width:12px; height:12px; background-color:#8B5FB5; border-radius:50%; margin-right:5px;"></span>Business Intelligence| YAML (e.g., `business-view-def.yml`, `business-metric.yml`) | **Business Metrics Logic:** Calculates business metrics from simulation results in two phases: Step 1 (component scope, complex arithmetic), Step 2 (global scope, aggregation/filtering).|
 
 ## Files Interaction
 
@@ -61,4 +61,4 @@ The outputs of GEMS consist of three main categories of objects: **Optimization
 
 - **Optimization Problem** represents the global mathematical formulation of the energy system simulation/optimization.
 - **Simulation Table** contains the raw results of the simulation or optimization, including the optimal values of decision variables and the values of expressions computed from them.
-- **Business Views** provide curated representations of the simulation or optimization results from a business-intelligence perspective, tailored to users [specific needs](../user-guide/outputs/business-view.md).
+- **Business Views** provide curated representations of the simulation or optimization results from a business-intelligence perspective, tailored to users [specific needs](../user-guide/outputs/view.md).