fixing in_depth guides index page

Author: mikibonacci

docs/source/in_depth/index.md

@@ -6,96 +6,5 @@ Comprehensive explanations of core concepts and advanced topics in `aiida-atomis
 :maxdepth: 2
 
 properties
-immutability
 storage_backends
-structure_of_the_code
-```
-
-## Core Concepts
-
-### 🏗️ **Property Types and Architecture**
-
-Understanding the property system in aiida-atomistic:
-- **Guide**: [Property Types](properties.md)
-- **Topics**: Global vs site vs computed properties, property formats, naming conventions
-- **Why it matters**: Understanding how to access and use structure properties effectively
-
-**Key takeaways:**
-- Individual site properties (singular: `charge`, `magmom`) vs computed arrays (plural: `charges`, `magmoms`)
-- Global properties apply to entire structure (`pbc`, `cell`, `hubbard`)
-- Computed properties are derived on-the-fly (`formula`, `kinds`, `dimensionality`)
-- Statistical properties for efficient queries (`max_charge`, `min_magmom`, etc.)
-- Clear property access patterns and formats
-
-### 🔒 **Immutability**
-
-Understanding the immutability model and its implications:
-- **Guide**: [Immutability in StructureData](immutability.md)
-- **Topics**: Immutable vs mutable structures, frozen data types, best practices
-- **Why it matters**: Data provenance, workflow reproducibility, AiiDA integration
-
-**Key takeaways:**
-- `StructureData` is immutable for provenance tracking
-- `StructureDataMutable` for construction and modification
-- How to work with frozen lists and sites
-- Converting between mutable and immutable structures
-
-### 💾 **Storage Backends**
-
-Understanding data storage strategies:
-- **Guide**: [Storage Backends](storage_backends.md)
-- **Topics**: Attribute-based vs repository-based storage, metadata-driven decisions, querying
-- **Why it matters**: Choosing the right backend for performance and scalability
-
-**Key takeaways:**
-- `StructureData`: All data in database attributes (queryable, simple)
-- `StructureDataRepository`: Arrays in `.npz` files, metadata in database (scalable)
-- Metadata controls storage location (`store_in="db"` vs `store_in="npz"`)
-- Trade-offs between queryability and storage efficiency
-
-### ⚙️ **Code Architecture**
-
-Internal structure and organization of the codebase:
-- **Guide**: [Structure of the Code](structure_of_the_code.md)
-- **Topics**: Module organization, class hierarchy, design patterns
-- **For**: Developers extending or contributing to aiida-atomistic
-
-## Advanced Topics
-
-### Property System Details
-
-How properties are implemented:
-- **Site properties**: Stored in `Site` model, accessed via `sites[i].property`
-- **Computed arrays**: Aggregated from sites using `@computed_field` decorators
-- **Global properties**: Stored in `StructureBaseModel`, apply to whole structure
-- **Validation**: Pydantic field validators and model validators
-
-### Performance Optimizations
-
-Structure operations and storage efficiency:
-- **Kind-based storage**: Compress repeated atoms for database efficiency
-- **Computed field caching**: Automatic memoization of expensive calculations
-- **Efficient copying**: Specialized methods for deep/shallow copies
-- **Lazy evaluation**: Properties computed only when accessed
-
-### Validation System
-
-Ensuring data integrity:
-- **Field-level validation**: Pydantic validators for each property
-- **Cross-property validation**: Model validators for consistency checks
-- **Kind validation**: Ensuring sites with same kind have same properties
-- **Site proximity checks**: Detecting atoms too close together
-- **Tolerance system**: Configurable precision for property comparisons
-
-## Related Documentation
-
-- **[How-to Guides](../how_to/index.md)**: Step-by-step instructions for common tasks
-  - [Creating Structures](../how_to/creation_mutation.md)
-  - [Working with Kinds](../how_to/kinds.md)
-  - [Magnetic Structures](../how_to/magnetic_structures.md)
-  - [Adding Properties](../how_to/dev_adding_properties.md)
-  - [Plugin Migration](../how_to/dev_plugin_migration.md)
-
-- **[Tutorials](../tutorials/index.md)**: Learn by example with complete workflows
-
-- **[Reference](../reference/api/index.md)**: Detailed API documentation
+```