docs: cleanup and extra references

.github/scripts/prepare_docs.py

@@ -3,7 +3,7 @@ import glob
 import re
 import shutil
 
-folders_to_copy = ["src", "scripts"]
+folders_to_copy = ["src", "scripts", "configs" ]
 for folder in folders_to_copy:
     if os.path.exists(folder):
         shutil.copytree(folder, f"docs/{folder}", dirs_exist_ok=True)
@@ -12,9 +12,9 @@ for filepath in glob.glob("docs/**/*.md", recursive=True):
     with open(filepath, "r", encoding="utf-8") as f:
         content = f.read()
 
-    # RULE A: Fix links pointing OUT to src/ or scripts/
+    # RULE A: Fix links pointing OUT to src/, scripts/, or configs/
     # Logic: Because the folders were moved one level deeper, we remove exactly ONE '../'
-    content = re.sub(r"\]\(\.\./((?:\.\./)*)(src|scripts)/([^)]*)\)", r"](\1\2/\3)", content)
+    content = re.sub(r"\]\(\.\./((?:\.\./)*)(src|scripts|configs)/([^)]*)\)", r"](\1\2/\3)", content)
 
     # RULE B: Fix links pointing FROM the copied files back TO the original docs/ folder
     # Logic: Since these files are now inside docs/, the 'docs/' segment in the path is redundant.

docs/README.md

@@ -9,6 +9,7 @@ For the core codebase, scripts, and contribution history, visit our [GitHub Repo
 - **[Installation Instructions](./DEVELOPMENT.md)**: Steps to set up your development environment locally or in a devcontainer using `uv`, including GPU configuration. For High-Performance Computing (HPC) setup details, see the **[HPC Guide](./HPC.md)**.
 - **[How to Run Experiments](./api/training.md)**: A complete guide on running training jobs, setting custom hyperparameters, and overriding config options using Hydra.
 - **[Results & Reproduction](./api/reproduction.md)**: Guide on how to access our public WandB training runs table and reproduce our training and evaluation phases (determining the best checkpoint vs. comparing architectures).
+- **[Contribution Guidelines](./CONTRIBUTING.md)**: Standards, rules, and best practices for developing and adding code to the repository.
 - **[Repository Structure](#repository-structure)**: Overview of the directories and files within the codebase.
 
 ## Repository Structure

docs/api/evaluation.md

@@ -54,3 +54,7 @@ python scripts/evaluate_checkpoints.py \
 ```
 
 This script scans the `checkpoints/` directory of the specified run and evaluates every `.flax` file it finds using the model's training morphology.
+
+---
+
+For a step-by-step walkthrough on using these evaluation phases to reproduce our project results, see the **[Results & Reproduction Guide](./reproduction.md)**.

docs/api/tracking.md

@@ -58,3 +58,7 @@ uv run python scripts/analysis/explore_tensorboard.py runs/your_run_name/
 ```
 
 See the detailed description in [`/scripts/analysis/README.md`](../../scripts/analysis/README.md).
+
+## Developer Logging API
+
+For details on the developer API of our internal logging library (how backend routing, checkpoint synchronization, and singleton initialization works), see the **[Experiment Logger API Guide](../../src/experiment_logger/README.md)**.

docs/api/training.md

@@ -6,6 +6,8 @@ This guide covers how to configure and run training experiments for the Brittle
 
 The project uses a modular configuration system powered by [Hydra](https://hydra.cc/). Instead of passing many command-line flags, you select and override configuration groups.
 
+For a detailed guide on the structure, validation, and usage of our Hydra configuration files, see the **[Brittle Star Configuration System Guide](../../configs/README.md)**.
+
 ### Creating a Custom Experiment
 
 1. **Create a new experiment file:**