diff --git a/agent/agent_utils.py b/agent/agent_utils.py
index c6ec4d5..3c5cb60 100644
--- a/agent/agent_utils.py
+++ b/agent/agent_utils.py
@@ -6,6 +6,8 @@
 from pathlib import Path
 from typing import List
 import fitz
+from import_deps import ModuleSet
+from graphlib import TopologicalSorter, CycleError
 import yaml
 
 from agent.class_types import AgentConfig
@@ -16,6 +18,7 @@
 UNIT_TESTS_INFO_HEADER = "\n\n>>> Here are the Unit Tests Information:\n"
 LINT_INFO_HEADER = "\n\n>>> Here is the Lint Information:\n"
 SPEC_INFO_HEADER = "\n\n>>> Here is the Specification Information:\n"
+IMPORT_DEPENDENCIES_HEADER = "\n\n>>> Here are the Import Dependencies:\n"
 # prefix components:
 space = "    "
 branch = "│   "
@@ -190,25 +193,97 @@ def _find_files_to_edit(base_dir: str, src_dir: str, test_dir: str) -> list[str]
     return files
 
 
-def get_target_edit_files(target_dir: str, src_dir: str, test_dir: str) -> list[str]:
+def ignore_cycles(graph: dict) -> list[str]:
+    """Ignore the cycles in the graph."""
+    ts = TopologicalSorter(graph)
+    try:
+        return list(ts.static_order())
+    except CycleError as e:
+        # print(f"Cycle detected: {e.args[1]}")
+        # You can either break the cycle by modifying the graph or handle it as needed.
+        # For now, let's just remove the first node in the cycle and try again.
+        cycle_nodes = e.args[1]
+        node_to_remove = cycle_nodes[0]
+        # print(f"Removing node {node_to_remove} to resolve cycle.")
+        graph.pop(node_to_remove, None)
+        return ignore_cycles(graph)
+
+
+def topological_sort_based_on_dependencies(
+    pkg_paths: list[str],
+) -> tuple[list[str], dict]:
+    """Topological sort based on dependencies."""
+    module_set = ModuleSet([str(p) for p in pkg_paths])
+
+    import_dependencies = {}
+    for path in sorted(module_set.by_path.keys()):
+        module_name = ".".join(module_set.by_path[path].fqn)
+        mod = module_set.by_name[module_name]
+        try:
+            imports = module_set.get_imports(mod)
+            import_dependencies[path] = set([str(x) for x in imports])
+        except Exception:
+            import_dependencies[path] = set()
+
+    import_dependencies_files = ignore_cycles(import_dependencies)
+
+    return import_dependencies_files, import_dependencies
+
+
+def get_target_edit_files(
+    local_repo: git.Repo,
+    src_dir: str,
+    test_dir: str,
+    latest_commit: str,
+    reference_commit: str,
+) -> tuple[list[str], dict]:
     """Find the files with functions with the pass statement."""
+    target_dir = str(local_repo.working_dir)
     files = _find_files_to_edit(target_dir, src_dir, test_dir)
     filtered_files = []
     for file_path in files:
-        with open(file_path, "r", encoding="utf-8", errors="ignore") as file:
+        with open(file_path, "r", encoding="utf-8-sig", errors="ignore") as file:
             content = file.read()
             if len(content.splitlines()) > 1500:
                 continue
             if "    pass" in content:
                 filtered_files.append(file_path)
+    # Change to reference commit to get the correct dependencies
+    local_repo.git.checkout(reference_commit)
+
+    topological_sort_files, import_dependencies = (
+        topological_sort_based_on_dependencies(filtered_files)
+    )
+    if len(topological_sort_files) != len(filtered_files):
+        if len(topological_sort_files) < len(filtered_files):
+            # Find the missing elements
+            missing_files = set(filtered_files) - set(topological_sort_files)
+            # Add the missing files to the end of the list
+            topological_sort_files = topological_sort_files + list(missing_files)
+        else:
+            raise ValueError(
+                "topological_sort_files should not be longer than filtered_files"
+            )
+    assert len(topological_sort_files) == len(
+        filtered_files
+    ), "all files should be included"
+
+    # change to latest commit
+    local_repo.git.checkout(latest_commit)
 
     # Remove the base_dir prefix
-    filtered_files = [
-        file.replace(target_dir, "").lstrip("/") for file in filtered_files
+    topological_sort_files = [
+        file.replace(target_dir, "").lstrip("/") for file in topological_sort_files
     ]
-    # Only keep python files
 
-    return filtered_files
+    # Remove the base_dir prefix from import dependencies
+    import_dependencies_without_prefix = {}
+    for key, value in import_dependencies.items():
+        key_without_prefix = key.replace(target_dir, "").lstrip("/")
+        value_without_prefix = [v.replace(target_dir, "").lstrip("/") for v in value]
+        import_dependencies_without_prefix[key_without_prefix] = value_without_prefix
+
+    return topological_sort_files, import_dependencies_without_prefix
 
 
 def get_message(
@@ -268,6 +343,20 @@ def get_message(
     return message_to_agent
 
 
+def update_message_with_dependencies(message: str, dependencies: list[str]) -> str:
+    """Update the message with the dependencies."""
+    if len(dependencies) == 0:
+        return message
+    import_dependencies_info = f"\n{IMPORT_DEPENDENCIES_HEADER}"
+    for dependency in dependencies:
+        with open(dependency, "r") as file:
+            import_dependencies_info += (
+                f"\nHere is the content of the file {dependency}:\n{file.read()}"
+            )
+    message += import_dependencies_info
+    return message
+
+
 def get_specification(specification_pdf_path: Path) -> str:
     """Get the reference for a given specification PDF path."""
     # TODO: after pdf_to_text is available, use it to extract the text from the PDF
diff --git a/agent/agents.py b/agent/agents.py
index 9255a9f..6e7d9d8 100644
--- a/agent/agents.py
+++ b/agent/agents.py
@@ -90,6 +90,11 @@ def run(
         sys.stdout = open(log_file, "a")
         sys.stderr = open(log_file, "a")
 
+        # Log the message
+        agent_message_log_file = log_dir / "agent_message.log"
+        with open(agent_message_log_file, "a") as f:
+            f.write(f"Message Sent: {message}\n\n")
+
         # Configure httpx and backoff logging
         handle_logging("httpx", log_file)
         handle_logging("backoff", log_file)
diff --git a/agent/cli.py b/agent/cli.py
index 905191b..8d06891 100644
--- a/agent/cli.py
+++ b/agent/cli.py
@@ -178,6 +178,10 @@ def run(
         ".agent.yaml",
         help="Path to the agent config file",
     ),
+    commit0_config_file: str = typer.Option(
+        ".commit0.yaml",
+        help="Path to the commit0 config file",
+    ),
     log_dir: str = typer.Option(
         str(RUN_AGENT_LOG_DIR.resolve()),
         help="Log directory to store the logs",
@@ -202,6 +206,7 @@ def run(
             override_previous_changes,
             backend,
             agent_config_file,
+            commit0_config_file,
             log_dir,
             max_parallel_repos,
             display_repo_progress_num,
@@ -212,6 +217,7 @@ def run(
             override_previous_changes,
             backend,
             agent_config_file,
+            commit0_config_file,
             log_dir,
             max_parallel_repos,
         )
diff --git a/agent/display.py b/agent/display.py
index a5f389c..53d01fe 100644
--- a/agent/display.py
+++ b/agent/display.py
@@ -17,6 +17,8 @@
 from rich.align import Align
 from collections import OrderedDict
 from types import TracebackType
+import json
+from datetime import datetime
 
 
 class RepoBox:
@@ -404,3 +406,29 @@ def __exit__(
             f"{'Total':<30} {self.total_time_spent:>13.2f}s {total_files:>18} {total_money:>13.2f}$"
         )
         print("-" * 80)
+
+        # Write summary to JSON file
+
+        summary_data = {
+            "timestamp": datetime.now().isoformat(),
+            "total_time_spent": self.total_time_spent,
+            "total_files_processed": total_files,
+            "total_money_spent": total_money,
+            "repositories": [
+                {
+                    "name": repo_name,
+                    "time_spent": self.end_time_per_repo[repo_name]
+                    - self.start_time_per_repo[repo_name],
+                    "files_processed": self.total_files_per_repo[repo_name],
+                    "money_spent": sum(
+                        self.repo_money_spent.get(repo_name, {}).values()
+                    ),
+                }
+                for repo_name in self.end_time_per_repo
+            ],
+        }
+
+        with open("processing_summary.json", "w") as json_file:
+            json.dump(summary_data, json_file, indent=4)
+
+        print("\nSummary has been written to processing_summary.json")
diff --git a/agent/run_agent.py b/agent/run_agent.py
index 3ef2a08..5315086 100644
--- a/agent/run_agent.py
+++ b/agent/run_agent.py
@@ -7,6 +7,7 @@
     create_branch,
     get_message,
     get_target_edit_files,
+    update_message_with_dependencies,
     get_lint_cmd,
     read_yaml_config,
 )
@@ -66,13 +67,6 @@ def run_agent_for_repo(
     repo_path = os.path.join(repo_base_dir, repo_name)
     repo_path = os.path.abspath(repo_path)
 
-    target_edit_files = get_target_edit_files(
-        repo_path, example["src_dir"], example["test"]["test_dir"]
-    )
-    # Call the commit0 get-tests command to retrieve test files
-    test_files_str = get_tests(repo_name, verbose=0)
-    test_files = sorted(list(set([i.split(":")[0] for i in test_files_str])))
-
     try:
         local_repo = Repo(repo_path)
     except Exception:
@@ -90,7 +84,6 @@ def run_agent_for_repo(
     # # if branch_name is not provided, create a new branch name based on agent_config
     # if branch is None:
     #     branch = args2string(agent_config)
-
     create_branch(local_repo, branch, example["base_commit"])
 
     # in cases where the latest commit of branch is not commit 0
@@ -99,6 +92,17 @@ def run_agent_for_repo(
     if latest_commit.hexsha != example["base_commit"] and override_previous_changes:
         local_repo.git.reset("--hard", example["base_commit"])
 
+    target_edit_files, import_dependencies = get_target_edit_files(
+        local_repo,
+        example["src_dir"],
+        example["test"]["test_dir"],
+        str(latest_commit),
+        example["reference_commit"],
+    )
+    # Call the commit0 get-tests command to retrieve test files
+    test_files_str = get_tests(repo_name, verbose=0)
+    test_files = sorted(list(set([i.split(":")[0] for i in test_files_str])))
+
     # prepare the log dir
     experiment_log_dir = (
         Path(log_dir)
@@ -158,6 +162,8 @@ def run_agent_for_repo(
             )
             for f in target_edit_files:
                 update_queue.put(("set_current_file", (repo_name, f)))
+                dependencies = import_dependencies[f]
+                message = update_message_with_dependencies(message, dependencies)
                 file_name = f.replace(".py", "").replace("/", "__")
                 file_log_dir = experiment_log_dir / file_name
                 lint_cmd = get_lint_cmd(repo_name, agent_config.use_lint_info)
@@ -176,6 +182,7 @@ def run_agent(
     override_previous_changes: bool,
     backend: str,
     agent_config_file: str,
+    commit0_config_file: str,
     log_dir: str,
     max_parallel_repos: int,
     display_repo_progress_num: int,
@@ -185,7 +192,7 @@ def run_agent(
 
     agent_config = AgentConfig(**config)
 
-    commit0_config = read_commit0_dot_file(".commit0.yaml")
+    commit0_config = read_commit0_dot_file(commit0_config_file)
 
     dataset = load_dataset(
         commit0_config["dataset_name"], split=commit0_config["dataset_split"]
diff --git a/agent/run_agent_no_rich.py b/agent/run_agent_no_rich.py
index c46ae2f..ec1334a 100644
--- a/agent/run_agent_no_rich.py
+++ b/agent/run_agent_no_rich.py
@@ -9,6 +9,7 @@
     create_branch,
     get_message,
     get_target_edit_files,
+    update_message_with_dependencies,
     get_lint_cmd,
     read_yaml_config,
 )
@@ -61,14 +62,6 @@ def run_agent_for_repo(
     repo_path = os.path.join(repo_base_dir, repo_name)
     repo_path = os.path.abspath(repo_path)
 
-    # get target files to edit and test files to run
-    target_edit_files = get_target_edit_files(
-        repo_path, example["src_dir"], example["test"]["test_dir"]
-    )
-    # Call the commit0 get-tests command to retrieve test files
-    test_files_str = get_tests(repo_name, verbose=0)
-    test_files = sorted(list(set([i.split(":")[0] for i in test_files_str])))
-
     try:
         local_repo = Repo(repo_path)
     except Exception:
@@ -95,6 +88,19 @@ def run_agent_for_repo(
     if latest_commit.hexsha != example["base_commit"] and override_previous_changes:
         local_repo.git.reset("--hard", example["base_commit"])
 
+    # get target files to edit and test files to run
+    target_edit_files, import_dependencies = get_target_edit_files(
+        local_repo,
+        example["src_dir"],
+        example["test"]["test_dir"],
+        str(latest_commit),
+        str(example["reference_commit"]),
+    )
+
+    # Call the commit0 get-tests command to retrieve test files
+    test_files_str = get_tests(repo_name, verbose=0)
+    test_files = sorted(list(set([i.split(":")[0] for i in test_files_str])))
+
     # prepare the log dir
     experiment_log_dir = (
         Path(log_dir)
@@ -139,6 +145,8 @@ def run_agent_for_repo(
                 agent_config, repo_path, test_dir=example["test"]["test_dir"]
             )
             for f in target_edit_files:
+                dependencies = import_dependencies[f]
+                message = update_message_with_dependencies(message, dependencies)
                 file_name = f.replace(".py", "").replace("/", "__")
                 file_log_dir = experiment_log_dir / file_name
                 lint_cmd = get_lint_cmd(repo_name, agent_config.use_lint_info)
@@ -151,6 +159,7 @@ def run_agent(
     override_previous_changes: bool,
     backend: str,
     agent_config_file: str,
+    commit0_config_file: str,
     log_dir: str,
     max_parallel_repos: int,
 ) -> None:
@@ -162,7 +171,7 @@ def run_agent(
 
     agent_config = AgentConfig(**config)
 
-    commit0_config = read_commit0_dot_file(".commit0.yaml")
+    commit0_config = read_commit0_dot_file(commit0_config_file)
 
     dataset = load_dataset(
         commit0_config["dataset_name"], split=commit0_config["dataset_split"]
diff --git a/pyproject.toml b/pyproject.toml
index 8befc62..7666711 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -11,6 +11,7 @@ requires-python = ">=3.11"
 dependencies = [
     "ruff>=0.6.4",
     "pre-commit>=3.8.0",
+    "import-deps>=0.3.0",
     "PyMuPDF>=1.24.5",
     "modal==0.64.95",
     "typer>=0.12.0",