diff --git a/.gitignore b/.gitignore
index 073b78763..7de3e4394 100644
--- a/.gitignore
+++ b/.gitignore
@@ -109,7 +109,6 @@ Output.txt
 research_outputs
 report.md
 src/data/*
-!src/data/.gitkeep
 # Logs
 *.log
 logs/
@@ -169,10 +168,6 @@ simulation_*summary.md
 !examples/benchmarks/**/run_*.sh
 !examples/benchmarks/**/*.py
 
-# Retain directory structure but ignore contents
-!data/benchmark_results/.gitkeep
-!data/optimization_results/.gitkeep
-
 **/.claude/settings.local.json
 
 # Folders created by Docker.
@@ -197,3 +192,7 @@ star_reviews_*.png
 web*.png
 tests/screenshots/
 screenshots/
+
+# Ignore cookiecutter-generated files.
+docker-compose.*.yml
+scripts/*.sh
diff --git a/cookiecutter-docker/cookiecutter.json b/cookiecutter-docker/cookiecutter.json
index 7bf7fb054..3b1b2714f 100644
--- a/cookiecutter-docker/cookiecutter.json
+++ b/cookiecutter-docker/cookiecutter.json
@@ -5,6 +5,5 @@
   "host_ip": "0.0.0.0",
   "host_network": false,
   "enable_gpu": true,
-  "enable_ollama": true,
   "enable_searxng": true
 }
diff --git a/cookiecutter-docker/hooks/post_gen_project.py b/cookiecutter-docker/hooks/post_gen_project.py
index 1ae53867d..bd1deeae5 100644
--- a/cookiecutter-docker/hooks/post_gen_project.py
+++ b/cookiecutter-docker/hooks/post_gen_project.py
@@ -14,6 +14,10 @@ def main():
     output_dir = compose_path.parent.absolute()
     compose_path.rename(output_dir.parent / COMPOSE_FILE_NAME)
 
+    # Move the entrypoint script to the scripts directory.
+    entrypoint_path = output_dir / "ollama_entrypoint.sh"
+    entrypoint_path.rename(output_dir.parent / "scripts" / "ollama_entrypoint.sh")
+
     # Delete the directory.
     shutil.rmtree(output_dir)
 
diff --git a/cookiecutter-docker/hooks/pre_prompt.py b/cookiecutter-docker/hooks/pre_prompt.py
index 27921ebf9..4b174cb04 100644
--- a/cookiecutter-docker/hooks/pre_prompt.py
+++ b/cookiecutter-docker/hooks/pre_prompt.py
@@ -3,12 +3,32 @@ import os
 import subprocess
 from typing import Any, Dict
 
+import cookiecutter.prompt
+
 
 def run_command(command: str):
     result = subprocess.run(command, shell=True, capture_output=True, text=True)
     return result.stdout.strip()
 
 
+def config_ollama(context: Dict[str, Any]) -> None:
+    """
+    Prompts the user for questions that are specific to Ollama. It is in a hook
+    so that we can run it only if Ollama is enabled.
+
+    """
+    enable_ollama = cookiecutter.prompt.read_user_yes_no("enable_ollama", True)
+    ollama_model = "gemma3:12b"
+    if enable_ollama:
+        # Ask ollama-specific questions.
+        ollama_model = cookiecutter.prompt.read_user_variable(
+            "ollama_model", ollama_model
+        )
+
+    context["_enable_ollama"] = enable_ollama
+    context["_ollama_model"] = ollama_model
+
+
 def check_gpu(context: Dict[str, Any]) -> None:
     """
     Check if the system has an NVIDIA or AMD GPU and set flags in the
@@ -45,6 +65,8 @@ def main() -> None:
     # Check GPU information and update the context only if running on Linux.
     if os.name == "posix" and os.uname().sysname == "Linux":
         check_gpu(context)
+    # Ollama-specific config.
+    config_ollama(context)
 
     # Save the updated context back to cookiecutter.json.
     with open("cookiecutter.json", "w") as config:
diff --git a/cookiecutter-docker/{{cookiecutter.config_name}}/docker-compose.{{cookiecutter.config_name}}.yml b/cookiecutter-docker/{{cookiecutter.config_name}}/docker-compose.{{cookiecutter.config_name}}.yml
index a9e329397..046b4f3be 100644
--- a/cookiecutter-docker/{{cookiecutter.config_name}}/docker-compose.{{cookiecutter.config_name}}.yml
+++ b/cookiecutter-docker/{{cookiecutter.config_name}}/docker-compose.{{cookiecutter.config_name}}.yml
@@ -20,7 +20,7 @@ services:
       # Web Interface Settings
       - LDR_WEB_PORT={{cookiecutter.host_port}}
       - LDR_WEB_HOST={{cookiecutter.host_ip}}
-      {%- if cookiecutter.enable_ollama %}
+      {%- if cookiecutter._enable_ollama %}
       - LDR_LLM_PROVIDER=ollama
       - LDR_LLM_OLLAMA_URL=http://ollama:11434
       {% endif %}
@@ -33,25 +33,36 @@ services:
       - ./local_collections/project_docs:/local_collections/project_docs/
       - ./local_collections/research_papers:/local_collections/research_papers/
     restart: unless-stopped
-    {%- if cookiecutter.enable_ollama or cookiecutter.enable_searxng %}
+    {%- if cookiecutter._enable_ollama or cookiecutter.enable_searxng %}
     depends_on:
-      {%- if cookiecutter.enable_ollama %}
-      - ollama
+      {%- if cookiecutter._enable_ollama %}
+      ollama:
+        condition: service_healthy
       {% endif %}
       {%- if cookiecutter.enable_searxng %}
-      - searxng
+      searxng:
+        condition: service_started
       {% endif %}
     {% endif %}
 
-  {%- if cookiecutter.enable_ollama %}
+  {%- if cookiecutter._enable_ollama %}
   ollama:
     {%- if cookiecutter.enable_gpu and cookiecutter._amd_gpu %}
     image: ollama/ollama:rocm
     {% else %}
     image: ollama/ollama:latest
     {% endif %}
+    container_name: ollama_service
+    entrypoint: [ "/scripts/ollama_entrypoint.sh" ]
+    healthcheck:
+      test: [ "CMD", "ollama", "show", "{{ cookiecutter._ollama_model }}" ]
+      interval: 10s
+      timeout: 5s
+      start_period: 10m
+      retries: 2
     volumes:
       - ollama_data:/root/.ollama
+      - ./scripts/:/scripts/
     {%- if not cookiecutter.host_network %}
     networks:
       - ldr-network
diff --git a/cookiecutter-docker/{{cookiecutter.config_name}}/ollama_entrypoint.sh b/cookiecutter-docker/{{cookiecutter.config_name}}/ollama_entrypoint.sh
new file mode 100755
index 000000000..950ac6e06
--- /dev/null
+++ b/cookiecutter-docker/{{cookiecutter.config_name}}/ollama_entrypoint.sh
@@ -0,0 +1,27 @@
+#!/bin/bash
+
+set -e
+
+# Start the main Ollama application
+ollama serve &
+
+# Wait for the Ollama application to be ready (optional, if necessary)
+while ! ollama ls; do
+  echo "Waiting for Ollama service to be ready..."
+  sleep 10
+done
+echo "Ollama service is ready."
+
+# Pull the model using ollama pull
+echo "Pulling the {{ cookiecutter._ollama_model }} with ollama pull..."
+ollama pull {{ cookiecutter._ollama_model }}
+# Check if the model was pulled successfully
+if [ $? -eq 0 ]; then
+  echo "Model pulled successfully."
+else
+  echo "Failed to pull model."
+  exit 1
+fi
+
+# Run ollama forever.
+sleep infinity
diff --git a/scripts/.gitkeep b/scripts/.gitkeep
new file mode 100644
index 000000000..e69de29bb