diff --git a/README.md b/README.md
new file mode 100644
index 0000000..f1dc622
--- /dev/null
+++ b/README.md
@@ -0,0 +1,121 @@
+# GitHub Data Pipeline
+
+This project builds a two-phase GitHub data pipeline:
+
+- Phase 1 samples repositories from GitHub Search and stores repository metadata.
+- Phase 2 reads the saved repositories, refreshes repository metadata, and downloads commit history from the current default branch.
+
+The project uses Poetry for dependency management and a `src` package layout for Python modules.
+
+## Project Layout
+
+- `src/github_datapipe/core/`
+  Shared config, GitHub API, runtime, and file IO helpers.
+- `src/github_datapipe/phases/phase1_repository_sampling/`
+  Phase 1 repository discovery and persistence.
+- `src/github_datapipe/phases/phase2_commit_ingestion/`
+  Phase 2 commit fetching and persistence.
+- `tests/`
+  Automated tests for the pipeline behavior.
+
+## Prerequisites
+
+- Python 3.12 installed locally
+- Poetry installed locally
+- GitHub personal access token stored in `.env` as:
+
+```env
+github_token=YOUR_TOKEN_HERE
+```
+
+## Install Dependencies
+
+From the project root, install the local environment with:
+
+```powershell
+poetry install
+```
+
+## Run Phase 1
+
+The default phase 1 command collects 10 repositories using the default search query from `src/github_datapipe/core/config.py`.
+
+```powershell
+poetry run github-datapipe sample-repos
+```
+
+Useful overrides:
+
+```powershell
+poetry run github-datapipe sample-repos --count 25
+poetry run github-datapipe sample-repos --count 25 --query "is:public stars:>50 size:>5000 archived:false"
+poetry run github-datapipe sample-repos --mode fresh
+```
+
+### Phase 1 Outputs
+
+After phase 1 completes, check:
+
+- `runs/<run_id>/phase1_repository_sampling/repos.jsonl`
+- `runs/<run_id>/phase1_repository_sampling/manifest.json`
+- `runs/seen_repo_ids.json`
+
+The command prints the generated `run_id`, which you will use for phase 2.
+
+## Run Phase 2
+
+Phase 2 consumes the saved phase 1 repositories and downloads commit history from each repository's current default branch.
+
+Run against a phase 1 run:
+
+```powershell
+poetry run github-datapipe fetch-commits --run-id <run_id>
+```
+
+Useful overrides:
+
+```powershell
+poetry run github-datapipe fetch-commits --run-id <run_id> --mode resume
+poetry run github-datapipe fetch-commits --run-id <run_id> --max-pages-per-repo 3
+poetry run github-datapipe fetch-commits --run-id <run_id> --per-page 50
+```
+
+### Phase 2 Defaults
+
+- `mode=refresh`
+- `per_page=100`
+- `max_pages_per_repo=1`
+
+The default `max_pages_per_repo=1` keeps the prototype small and limits commit downloads to the first page for each repository.
+
+### Phase 2 Outputs
+
+After phase 2 completes, check:
+
+- `runs/<run_id>/phase2_commit_ingestion/commits/commits-0001.jsonl`
+- `runs/<run_id>/phase2_commit_ingestion/repo_status.jsonl`
+- `runs/<run_id>/phase2_commit_ingestion/manifest.json`
+
+## Run Tests
+
+Run the automated tests with:
+
+```powershell
+poetry run pytest -q
+```
+
+## Alternate CLI Invocation
+
+If the Poetry script entrypoint is not available yet, run the CLI module directly:
+
+```powershell
+poetry run python -m github_datapipe.cli sample-repos
+poetry run python -m github_datapipe.cli fetch-commits --run-id <run_id>
+```
+
+## Notes
+
+- Phase 1 currently uses deterministic GitHub Search traversal rather than randomized sampling.
+- Phase 2 stores one normalized commit per JSONL line.
+- Resume mode in phase 2 skips repositories already marked `complete`.
+- Truncated repositories are marked as `success_with_warning` when the page cap is reached.
diff --git a/pyproject.toml b/pyproject.toml
index eaf7165..3911a03 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -16,12 +16,16 @@ dependencies = [
 ]
 
 [project.scripts]
-github-datapipe = "github_datapipe.extract_repos:main"
+github-datapipe = "github_datapipe.cli:main"
 
+[tool.poetry]
+packages = [
+    { include = "github_datapipe", from = "src" }
+]
 
 [build-system]
 requires = ["poetry-core>=2.0.0,<3.0.0"]
 build-backend = "poetry.core.masonry.api"
 
 [tool.pytest.ini_options]
-pythonpath = ["src"]
\ No newline at end of file
+pythonpath = ["src"]
diff --git a/src/github_datapipe/__init__.py b/src/github_datapipe/__init__.py
index e69de29..0b52f1b 100644
--- a/src/github_datapipe/__init__.py
+++ b/src/github_datapipe/__init__.py
@@ -0,0 +1 @@
+"""GitHub data pipeline package."""
diff --git a/src/github_datapipe/cli.py b/src/github_datapipe/cli.py
new file mode 100644
index 0000000..5f499c7
--- /dev/null
+++ b/src/github_datapipe/cli.py
@@ -0,0 +1,165 @@
+from __future__ import annotations
+
+import argparse
+from pathlib import Path
+
+from github_datapipe.core.config import GithubConfig
+# Phase1 is concerned with querying the repo data
+from github_datapipe.phases.phase1_repository_sampling.service import (
+    SampleReposOptions,
+    resolve_query,
+    sample_repositories,
+)
+# Phase 2 is concerned with downloading the commit data for repos collected in phase 1
+from github_datapipe.phases.phase2_commit_ingestion.service import (
+    FetchCommitsOptions,
+    fetch_commits,
+)
+
+
+def build_parser() -> argparse.ArgumentParser:
+    parser = argparse.ArgumentParser(description="GitHub data pipeline CLI")
+    subparsers = parser.add_subparsers(dest="command", required=True)
+
+    sample_parser = subparsers.add_parser(
+        "sample-repos",
+        help="Collect repositories from GitHub Search and save phase 1 outputs.",
+    )
+    sample_parser.add_argument(
+        "--count",
+        type=int,
+        default=GithubConfig.default_repo_count,
+        help=f"Number of repositories to sample. Defaults to {GithubConfig.default_repo_count}.",
+    )
+    sample_parser.add_argument(
+        "--query",
+        type=str,
+        default=None,
+        help="Optional raw GitHub repository search query. Replaces config defaults when provided.",
+    )
+    sample_parser.add_argument(
+        "--output-root",
+        type=Path,
+        default=Path(GithubConfig.default_output_root),
+        help=f"Directory where run outputs are stored. Defaults to `{GithubConfig.default_output_root}`.",
+    )
+    sample_parser.add_argument(
+        "--mode",
+        choices=("append-deduped", "fresh"),
+        default="append-deduped",
+        help="Whether to dedupe against the persisted seen-repo index or start a fresh phase-1 run.",
+    )
+    sample_parser.add_argument(
+        "--per-page",
+        type=int,
+        default=GithubConfig.default_per_page,
+        help=f"GitHub Search page size. Defaults to {GithubConfig.default_per_page}.",
+    )
+    sample_parser.add_argument(
+        "--run-id",
+        type=str,
+        default=None,
+        help="Optional run identifier. If omitted, a run id is generated automatically.",
+    )
+
+    commit_parser = subparsers.add_parser(
+        "fetch-commits",
+        help="Fetch commit history for repositories collected in phase 1.",
+    )
+    commit_input = commit_parser.add_mutually_exclusive_group(required=True)
+    commit_input.add_argument(
+        "--run-id",
+        type=str,
+        help="Run identifier whose phase 1 repository dataset should be consumed.",
+    )
+    commit_input.add_argument(
+        "--repos-file",
+        type=Path,
+        help="Path to a phase 1 repos.jsonl file.",
+    )
+    commit_parser.add_argument(
+        "--output-root",
+        type=Path,
+        default=Path(GithubConfig.default_output_root),
+        help=f"Directory where run outputs are stored. Defaults to `{GithubConfig.default_output_root}`.",
+    )
+    commit_parser.add_argument(
+        "--mode",
+        choices=("refresh", "resume"),
+        default="refresh",
+        help="Whether to fetch all repositories from scratch or skip those already marked complete.",
+    )
+    commit_parser.add_argument(
+        "--max-pages-per-repo",
+        type=int,
+        default=GithubConfig.default_max_pages_per_repo,
+        help=(
+            "Maximum number of commit pages to fetch per repository. "
+            f"Defaults to {GithubConfig.default_max_pages_per_repo}."
+        ),
+    )
+    commit_parser.add_argument(
+        "--per-page",
+        type=int,
+        default=GithubConfig.default_per_page,
+        help=f"GitHub commit page size. Defaults to {GithubConfig.default_per_page}.",
+    )
+    commit_parser.add_argument(
+        "--retry-count",
+        type=int,
+        default=GithubConfig.default_retry_count,
+        help=f"Number of retries for repository metadata and commit requests. Defaults to {GithubConfig.default_retry_count}.",
+    )
+
+    return parser
+
+
+def main() -> int:
+    parser = build_parser()
+    args = parser.parse_args()
+
+    if args.command == "sample-repos":
+        options = SampleReposOptions(
+            count=args.count,
+            output_root=args.output_root,
+            query=resolve_query(args.query),
+            per_page=args.per_page,
+            mode=args.mode,
+            run_id=args.run_id,
+        )
+        result = sample_repositories(options)
+        print(f"Run ID: {result['run_id']}")
+        print(f"Collected repositories: {result['count_collected']}")
+        print(f"Repositories file: {result['repos_path']}")
+        print(f"Manifest file: {result['manifest_path']}")
+        if result["seen_index_path"] is not None:
+            print(f"Seen repo index: {result['seen_index_path']}")
+        return 0
+
+    if args.command == "fetch-commits":
+        options = FetchCommitsOptions(
+            output_root=args.output_root,
+            run_id=args.run_id,
+            repos_file=args.repos_file,
+            mode=args.mode,
+            per_page=args.per_page,
+            max_pages_per_repo=args.max_pages_per_repo,
+            retry_count=args.retry_count,
+        )
+        result = fetch_commits(options)
+        print(f"Run ID: {result['run_id']}")
+        print(f"Processed repositories: {result['processed_repositories']}")
+        print(f"Completed repositories: {result['completed_repositories']}")
+        print(f"Warning repositories: {result['warning_repositories']}")
+        print(f"Failed repositories: {result['failed_repositories']}")
+        print(f"Commits file: {result['commits_path']}")
+        print(f"Status file: {result['status_path']}")
+        print(f"Manifest file: {result['manifest_path']}")
+        return 0
+
+    parser.error(f"Unsupported command: {args.command}")
+    return 1
+
+
+if __name__ == "__main__":
+    raise SystemExit(main())
diff --git a/src/github_datapipe/core/__init__.py b/src/github_datapipe/core/__init__.py
new file mode 100644
index 0000000..db1fbb7
--- /dev/null
+++ b/src/github_datapipe/core/__init__.py
@@ -0,0 +1 @@
+"""Shared building blocks for GitHub pipeline phases."""
diff --git a/src/github_datapipe/config.py b/src/github_datapipe/core/config.py
similarity index 74%
rename from src/github_datapipe/config.py
rename to src/github_datapipe/core/config.py
index ac85ebf..0ca16d2 100644
--- a/src/github_datapipe/config.py
+++ b/src/github_datapipe/core/config.py
@@ -4,7 +4,7 @@ from dataclasses import dataclass
 from pathlib import Path
 
 
-@dataclass(frozen=True) # This makes the class immutable so in the process, we do not accidently change the variable values of this
+@dataclass(frozen=True)
 class GithubConfig:
     base_url: str = "https://api.github.com"
     api_version: str = "2022-11-28"
@@ -13,9 +13,9 @@ class GithubConfig:
     default_per_page: int = 100
     default_output_root: str = "runs"
     default_query: str = "is:public stars:>10 size:>1000 archived:false fork:false created:>2025-07-15"
+    default_max_pages_per_repo: int = 1
+    default_retry_count: int = 2
     user_agent: str = "github-datapipe/0.1.0"
 
 
-
-
-ROOT_DIR = Path(__file__).resolve().parent
+ROOT_DIR = Path(__file__).resolve().parents[2]
diff --git a/src/github_datapipe/core/github_api.py b/src/github_datapipe/core/github_api.py
new file mode 100644
index 0000000..9f91df3
--- /dev/null
+++ b/src/github_datapipe/core/github_api.py
@@ -0,0 +1,54 @@
+from __future__ import annotations
+
+from typing import Any
+
+import requests
+
+from github_datapipe.core.config import GithubConfig
+
+
+class GithubApiError(RuntimeError):
+    """Raised when GitHub responds with an error payload."""
+
+
+class GithubApiClient:
+    def __init__(self, token: str, session: requests.Session | None = None) -> None:
+        self._session = session or requests.Session()
+        self._session.headers.update(
+            {
+                "Accept": "application/vnd.github+json",
+                "Authorization": f"Bearer {token}",
+                "X-GitHub-Api-Version": GithubConfig.api_version,
+                "User-Agent": GithubConfig.user_agent,
+            }
+        )
+
+    def search_repositories(self, query: str, page: int, per_page: int) -> dict[str, Any]:
+        return self._get_json(
+            GithubConfig.search_repositories_endpoint,
+            params={"q": query, "page": page, "per_page": per_page},
+        )
+
+    def get_repository(self, full_name: str) -> dict[str, Any]:
+        return self._get_json(f"/repos/{full_name}")
+
+    def list_commits(self, full_name: str, branch: str, page: int, per_page: int) -> list[dict[str, Any]]:
+        return self._get_json(
+            f"/repos/{full_name}/commits",
+            params={"sha": branch, "page": page, "per_page": per_page},
+        )
+
+    def _get_json(self, path: str, params: dict[str, Any] | None = None) -> Any:
+        response = self._session.get(
+            f"{GithubConfig.base_url}{path}",
+            params=params,
+            timeout=30,
+        )
+        if response.status_code >= 400:
+            try:
+                payload = response.json()
+            except ValueError:
+                payload = {"message": response.text}
+            message = payload.get("message", "GitHub API request failed")
+            raise GithubApiError(f"GitHub request failed ({response.status_code}): {message}")
+        return response.json()
diff --git a/src/github_datapipe/core/io.py b/src/github_datapipe/core/io.py
new file mode 100644
index 0000000..55e6f6a
--- /dev/null
+++ b/src/github_datapipe/core/io.py
@@ -0,0 +1,43 @@
+from __future__ import annotations
+
+import json
+from pathlib import Path
+from typing import Any, Iterable
+
+
+def write_json(path: Path, payload: Any) -> None:
+    path.parent.mkdir(parents=True, exist_ok=True)
+    path.write_text(json.dumps(payload, indent=2), encoding="utf-8")
+
+
+def write_jsonl(path: Path, rows: Iterable[dict[str, Any]]) -> None:
+    path.parent.mkdir(parents=True, exist_ok=True)
+    with path.open("w", encoding="utf-8") as handle:
+        for row in rows:
+            handle.write(json.dumps(row))
+            handle.write("\n")
+
+
+def append_jsonl(path: Path, rows: Iterable[dict[str, Any]]) -> int:
+    path.parent.mkdir(parents=True, exist_ok=True)
+    count = 0
+    with path.open("a", encoding="utf-8") as handle:
+        for row in rows:
+            handle.write(json.dumps(row))
+            handle.write("\n")
+            count += 1
+    return count
+
+
+def read_json(path: Path) -> Any:
+    return json.loads(path.read_text(encoding="utf-8"))
+
+
+def read_jsonl(path: Path) -> list[dict[str, Any]]:
+    if not path.exists():
+        return []
+    rows: list[dict[str, Any]] = []
+    for line in path.read_text(encoding="utf-8").splitlines():
+        if line.strip():
+            rows.append(json.loads(line))
+    return rows
diff --git a/src/github_datapipe/core/runtime.py b/src/github_datapipe/core/runtime.py
new file mode 100644
index 0000000..4a33100
--- /dev/null
+++ b/src/github_datapipe/core/runtime.py
@@ -0,0 +1,24 @@
+from __future__ import annotations
+
+import os
+from datetime import UTC, datetime
+from uuid import uuid4
+
+from dotenv import load_dotenv
+
+load_dotenv()
+
+
+def require_github_token() -> str:
+    github_token = os.getenv("github_token")
+    if not github_token:
+        raise ValueError("GitHub token is not available in .env as `github_token`.")
+    return github_token
+
+
+def build_run_id() -> str:
+    return f"run-{datetime.now(tz=UTC).strftime('%Y%m%dT%H%M%SZ')}-{uuid4().hex[:8]}"
+
+
+def utc_now() -> str:
+    return datetime.now(tz=UTC).isoformat()
diff --git a/src/github_datapipe/extract_repos.py b/src/github_datapipe/extract_repos.py
deleted file mode 100644
index 09929ae..0000000
--- a/src/github_datapipe/extract_repos.py
+++ /dev/null
@@ -1,286 +0,0 @@
-from __future__ import annotations
-
-import json
-import os
-from dataclasses import dataclass
-from datetime import UTC, datetime
-from pathlib import Path
-from typing import Any
-from uuid import uuid4
-
-import requests
-from dotenv import load_dotenv
-
-from github_datapipe.config import GithubConfig
-
-load_dotenv()
-
-
-class GithubApiError(RuntimeError):
-    """Raised when GitHub responds with an error payload."""
-
-
-@dataclass(frozen=True)
-class SampleReposOptions:
-    """
-        To set configuration options for the GitHub repository sampling run.
-        Attributes:
-            1. count (int): The total number of unique repositories to collect. Must be > 0. Defaults to GithubConfig.default_repo_count
-            2. output_root: The base directory where the run folder will be created to store the search repository data.
-            3. query: The github search string using github offered query params.
-            4. per_page: The number of results to fetch per API call. Max is 100.
-            5. mode: 'fresh' (starting a fresh run) or "append-deduped" (if you want to resume half-done previous run and avoid duplicates).
-            6. run_id: To keep a trace of current run by giving it a unique id.
-    """
-    count: int = GithubConfig.default_repo_count
-    output_root: Path = Path(GithubConfig.default_output_root)
-    query: str = GithubConfig.default_query
-    per_page: int = GithubConfig.default_per_page
-    mode: str = "append-deduped"
-    run_id: str | None = None
-
-
-def resolve_query(query_override: str | None) -> str:
-    """ To override default query params with user inserted query params. """
-    return query_override.strip() if query_override else GithubConfig.default_query
-
-
-class GithubRepoSampler:
-    def __init__(self, token: str, session: requests.Session | None = None) -> None:
-        """
-            Everytime an instance of GithubRepoSampler is created, this method will be called first to open a session and set headers.
-            Args:
-                token (str): A valid GitHub Personal Access Token (PAT).
-                session (requests.Session | None, optional): An existing session to use. If None, a new session is created.
-        """
-        self._session = session or requests.Session()
-        self._session.headers.update(
-            {
-                "Accept": "application/vnd.github+json",
-                "Authorization": f"Bearer {token}",
-                "X-GitHub-Api-Version": GithubConfig.api_version,
-                "User-Agent": GithubConfig.user_agent,
-            }
-        )
-
-    def search_repositories(self, query: str, page: int, per_page: int) -> dict[str, Any]:
-        """
-            Calls github's /search/repositories endpoint passing query params and other.
-
-            Args:
-                query (str): The GitHub-formatted search query string.
-                page (int): The specific page of results to fetch.
-                per_page (int): The number of items to return per page (max 100).
-
-            Returns:
-                dict[str, Any]: The raw JSON payload returned by the GitHub API.
-
-            Raises:
-                GithubApiError: If the API responds with an HTTP status code >= 400 
-        """
-        response = self._session.get(
-            f"{GithubConfig.base_url}{GithubConfig.search_repositories_endpoint}",
-            params={"q": query, "page": page, "per_page": per_page},
-            timeout=30,
-        )
-        if response.status_code >= 400:
-            try:
-                payload = response.json()
-            except ValueError:
-                payload = {"message": response.text}
-            message = payload.get("message", "GitHub API request failed")
-            raise GithubApiError(f"GitHub search failed ({response.status_code}): {message}")
-        return response.json()
-
-
-def sample_repositories(options: SampleReposOptions) -> dict[str, Any]:
-    """
-        Orchestrates the end-to-end execution of a GitHub repository data pull.
-
-        This function handles the complete lifecycle of a sampling run: validating credentials,
-        setting up the local file system for the run, managing state to prevent duplicate 
-        downloads, paginating through the GitHub Search API, and saving the normalized data.
-
-        Effects:
-            - Creates a timestamped run directory inside `options.output_root`.
-            - Writes newly fetched repository data to `repos.jsonl`.
-            - Writes or updates a global `seen_repo_ids.json` tracker file.
-            - Writes a `manifest.json` logging the run's parameters and results.
-
-        Args:
-            options (SampleReposOptions): The configuration parameters for the run.
-
-        Returns:
-            dict[str, Any]: A summary dictionary containing the `run_id`, the total 
-                `count_collected`, and the absolute paths to the generated output files.
-    """
-    # 1. SETUP: Validate the token and creds
-    github_token = os.getenv("github_token")
-    if not github_token:
-        raise ValueError("GitHub token is not available in .env as `github_token`.")
-
-    if options.count <= 0:
-        raise ValueError("`count` must be greater than 0.")
-
-    # 2. FILE SYSTEM: Create isolated folders for this specific run
-    run_id = options.run_id or build_run_id()
-    output_root = options.output_root.resolve() # returns an absolute path
-    run_root = output_root / run_id # isolated folder created for one single execution (or "run") of this script.
-    phase1_root = run_root / "phase1" # the search phase is phase 1
-    phase1_root.mkdir(parents=True, exist_ok=True) 
-
-    # Define exact file paths for where data will live
-    seen_index_path = output_root / "seen_repo_ids.json" # Notes the last seen repo's id
-    repos_path = phase1_root / "repos.jsonl" # Actual repo metadata
-    manifest_path = phase1_root / "manifest.json" # log entry
-
-    # 3. STATE MGMT: seen_repo_ids will make sure that duplicated data doesn't end up in the result
-    seen_repo_ids = set() if options.mode == "fresh" else load_seen_repo_ids(seen_index_path)
-    current_run_seen_repo_ids: set[int] = set()
-
-    # 4. NETWORK SETUP: Initialize the session wrapper
-    sampler = GithubRepoSampler(token=github_token)
-    accepted_repos: list[dict[str, Any]] = []
-    page = 1
-    total_count: int | None = None
-
-    # 5. THE MAIN LOOP: Keep fetching until the requested target count is hit
-    while len(accepted_repos) < options.count:
-        payload = sampler.search_repositories(
-            query=options.query,
-            page=page,
-            per_page=options.per_page,
-        )
-        # Github Search API response = JSON Object containing { search metadata, items: [{ repo obj1 }, { repo obj 2} ...] }
-        items = payload.get("items", []) 
-        total_count = payload.get("total_count", total_count) # the number of the repos matching your query at exact moment in time
-        
-        # Break safety: If GitHub returns an empty list, we've exhausted all results of current api call
-        if not items:
-            break
-
-        sampled_at = utc_now() # to keep note of current time incase we need to revise it
-
-        # Process each repository in the current result present in items
-        for repo in items:
-            repo_id = int(repo["id"])
-            if repo_id in seen_repo_ids or repo_id in current_run_seen_repo_ids:
-                continue
-
-            normalized_repo = normalize_repo_record(
-                repo=repo,
-                run_id=run_id,
-                sample_query=options.query,
-                sample_page=page,
-                sampled_at=sampled_at,
-            )
-            accepted_repos.append(normalized_repo)
-            current_run_seen_repo_ids.add(repo_id)
-
-            if len(accepted_repos) >= options.count:
-                break
-
-        page += 1
-
-    write_jsonl(repos_path, accepted_repos)
-    if options.mode != "fresh":
-        seen_repo_ids.update(current_run_seen_repo_ids)
-        write_json(seen_index_path, sorted(seen_repo_ids))
-
-    # manifest is a log object that denotes what kind of input was given to achieve certain output.
-    manifest = {
-        "run_id": run_id,
-        "command": "sample-repos",
-        "resolved_query": options.query,
-        "count_requested": options.count,
-        "count_collected": len(accepted_repos),
-        "per_page": options.per_page,
-        "mode": options.mode,
-        "page_count_scanned": max(page - 1, 0),
-        "github_total_count": total_count,
-        "output_files": {
-            "repos_jsonl": str(repos_path),
-            "seen_repo_ids_json": str(seen_index_path) if options.mode != "fresh" else None,
-        },
-        "sampled_at": utc_now(),
-    }
-    write_json(manifest_path, manifest)
-
-    return {
-        "run_id": run_id,
-        "count_collected": len(accepted_repos),
-        "repos_path": repos_path,
-        "manifest_path": manifest_path,
-        "seen_index_path": seen_index_path if options.mode != "fresh" else None,
-    }
-
-
-def normalize_repo_record(
-    repo: dict[str, Any],
-    run_id: str,
-    sample_query: str,
-    sample_page: int,
-    sampled_at: str,
-) -> dict[str, Any]:
-    
-    """
-        Extracts and flattens relevant fields from a raw GitHub repository payload.
-
-        Args:
-            repo (dict[str, Any]): The raw JSON dictionary for a single repository 
-                as returned by the GitHub API.
-            run_id (str): The unique identifier for the current sampling run.
-            sample_query (str): The search string used to find this repository.
-            sample_page (int): The pagination page number this repository was found on.
-            sampled_at (str): ISO-8601 formatted timestamp of when the record was fetched.
-
-        Returns:
-            dict[str, Any]: A flat dictionary containing the filtered repository metrics 
-            (e.g., repo_id, language, stargazers_count, size_kb) and traceability data.
-    """
-    return {
-        "run_id": run_id,
-        "repo_id": repo["id"],
-        "full_name": repo["full_name"],
-        "html_url": repo["html_url"],
-        "api_url": repo["url"],
-        "default_branch": repo.get("default_branch"),
-        "language": repo.get("language"),
-        "description": repo.get("description"),
-        "stargazers_count": repo.get("stargazers_count"),
-        "size_kb": repo.get("size"),
-        "fork": repo.get("fork"),
-        "archived": repo.get("archived"),
-        "visibility": repo.get("visibility"),
-        "sample_query": sample_query,
-        "sample_page": sample_page,
-        "sampled_at": sampled_at,
-    }
-
-
-def load_seen_repo_ids(path: Path) -> set[int]:
-    if not path.exists():
-        return set()
-    payload = json.loads(path.read_text(encoding="utf-8"))
-    return {int(repo_id) for repo_id in payload}
-
-
-def write_json(path: Path, payload: Any) -> None:
-    path.parent.mkdir(parents=True, exist_ok=True)
-    path.write_text(json.dumps(payload, indent=2), encoding="utf-8")
-
-
-def write_jsonl(path: Path, rows: list[dict[str, Any]]) -> None:
-    path.parent.mkdir(parents=True, exist_ok=True)
-    with path.open("w", encoding="utf-8") as handle:
-        for row in rows:
-            handle.write(json.dumps(row))
-            handle.write("\n")
-
-
-def build_run_id() -> str:
-    return f"run-{datetime.now(tz=UTC).strftime('%Y%m%dT%H%M%SZ')}-{uuid4().hex[:8]}"
-
-
-def utc_now() -> str:
-    return datetime.now(tz=UTC).isoformat()
\ No newline at end of file
diff --git a/src/github_datapipe/main.py b/src/github_datapipe/main.py
deleted file mode 100644
index 602832c..0000000
--- a/src/github_datapipe/main.py
+++ /dev/null
@@ -1,86 +0,0 @@
-from __future__ import annotations
-
-import argparse
-from pathlib import Path
-
-from github_datapipe.config import GithubConfig
-from github_datapipe.extract_repos import SampleReposOptions, resolve_query, sample_repositories
-
-### parser that unpacks the command line args passed as queries and 
-def build_parser() -> argparse.ArgumentParser:
-    parser = argparse.ArgumentParser(description="GitHub data pipeline CLI")
-    subparsers = parser.add_subparsers(dest="command", required=True)
-
-    sample_parser = subparsers.add_parser(
-        "sample-repos",
-        help="Collect repositories from GitHub Search and save phase 1 outputs.",
-    )
-    sample_parser.add_argument(
-        "--count",
-        type=int,
-        default=GithubConfig.default_repo_count,
-        help=f"Number of repositories to sample. Defaults to {GithubConfig.default_repo_count}.",
-    )
-    sample_parser.add_argument(
-        "--query",
-        type=str,
-        default=None,
-        help="Optional raw GitHub repository search query. Replaces config defaults when provided.",
-    )
-    sample_parser.add_argument(
-        "--output-root",
-        type=Path,
-        default=Path(GithubConfig.default_output_root),
-        help=f"Directory where run outputs are stored. Defaults to `{GithubConfig.default_output_root}`.",
-    )
-    sample_parser.add_argument(
-        "--mode",
-        choices=("append-deduped", "fresh"),
-        default="append-deduped",
-        help="Whether to dedupe against the persisted seen-repo index or start a fresh phase-1 run.",
-    )
-    sample_parser.add_argument(
-        "--per-page",
-        type=int,
-        default=GithubConfig.default_per_page,
-        help=f"GitHub Search page size. Defaults to {GithubConfig.default_per_page}.",
-    )
-    sample_parser.add_argument(
-        "--run-id",
-        type=str,
-        default=None,
-        help="Optional run identifier. If omitted, a run id is generated automatically.",
-    )
-
-    return parser
-
-
-def main() -> int:
-    parser = build_parser()
-    args = parser.parse_args()
-
-    if args.command == "sample-repos":
-        options = SampleReposOptions(
-            count=args.count,
-            output_root=args.output_root,
-            query=resolve_query(args.query),
-            per_page=args.per_page,
-            mode=args.mode,
-            run_id=args.run_id,
-        )
-        # result will return output from the extract repo's sample_repositories
-        result = sample_repositories(options)
-        print(f"Run ID: {result['run_id']}")
-        print(f"Collected repositories: {result['count_collected']}")
-        print(f"Repositories file: {result['repos_path']}")
-        print(f"Manifest file: {result['manifest_path']}")
-        if result["seen_index_path"] is not None:
-            print(f"Seen repo index: {result['seen_index_path']}")
-        return 0
-
-    parser.error(f"Unsupported command: {args.command}")
-    return 1
-
-
-if __name__ == "__main__":
-    raise SystemExit(main())
diff --git a/src/github_datapipe/phases/__init__.py b/src/github_datapipe/phases/__init__.py
new file mode 100644
index 0000000..fe0f601
--- /dev/null
+++ b/src/github_datapipe/phases/__init__.py
@@ -0,0 +1 @@
+"""Pipeline phases for repository sampling and commit ingestion."""
diff --git a/src/github_datapipe/phases/phase1_repository_sampling/__init__.py b/src/github_datapipe/phases/phase1_repository_sampling/__init__.py
new file mode 100644
index 0000000..2cb99da
--- /dev/null
+++ b/src/github_datapipe/phases/phase1_repository_sampling/__init__.py
@@ -0,0 +1 @@
+"""Phase 1: repository discovery and persistence."""
diff --git a/src/github_datapipe/phases/phase1_repository_sampling/service.py b/src/github_datapipe/phases/phase1_repository_sampling/service.py
new file mode 100644
index 0000000..8538ad2
--- /dev/null
+++ b/src/github_datapipe/phases/phase1_repository_sampling/service.py
@@ -0,0 +1,148 @@
+from __future__ import annotations
+
+from dataclasses import dataclass
+from pathlib import Path
+from typing import Any
+
+from github_datapipe.core.config import GithubConfig
+from github_datapipe.core.github_api import GithubApiClient
+from github_datapipe.core.io import read_json, write_json, write_jsonl
+from github_datapipe.core.runtime import build_run_id, require_github_token, utc_now
+
+
+@dataclass(frozen=True)
+class SampleReposOptions:
+    count: int = GithubConfig.default_repo_count
+    output_root: Path = Path(GithubConfig.default_output_root)
+    query: str = GithubConfig.default_query
+    per_page: int = GithubConfig.default_per_page
+    mode: str = "append-deduped"
+    run_id: str | None = None
+
+
+def resolve_query(query_override: str | None) -> str:
+    return query_override.strip() if query_override else GithubConfig.default_query
+
+
+def sample_repositories(options: SampleReposOptions) -> dict[str, Any]:
+    token = require_github_token()
+    if options.count <= 0:
+        raise ValueError("`count` must be greater than 0.")
+
+    run_id = options.run_id or build_run_id()
+    output_root = options.output_root.resolve()
+    run_root = output_root / run_id
+    phase_root = run_root / "phase1_repository_sampling"
+    phase_root.mkdir(parents=True, exist_ok=True)
+
+    seen_index_path = output_root / "seen_repo_ids.json"
+    repos_path = phase_root / "repos.jsonl"
+    manifest_path = phase_root / "manifest.json"
+
+    seen_repo_ids = set() if options.mode == "fresh" else load_seen_repo_ids(seen_index_path)
+    current_run_seen_repo_ids: set[int] = set()
+
+    client = GithubApiClient(token=token)
+    accepted_repos: list[dict[str, Any]] = []
+    page = 1
+    total_count: int | None = None
+
+    while len(accepted_repos) < options.count:
+        payload = client.search_repositories(
+            query=options.query,
+            page=page,
+            per_page=options.per_page,
+        )
+        items = payload.get("items", [])
+        total_count = payload.get("total_count", total_count)
+
+        if not items:
+            break
+
+        sampled_at = utc_now()
+        for repo in items:
+            repo_id = int(repo["id"])
+            if repo_id in seen_repo_ids or repo_id in current_run_seen_repo_ids:
+                continue
+
+            accepted_repos.append(
+                normalize_repo_record(
+                    repo=repo,
+                    run_id=run_id,
+                    sample_query=options.query,
+                    sample_page=page,
+                    sampled_at=sampled_at,
+                )
+            )
+            current_run_seen_repo_ids.add(repo_id)
+
+            if len(accepted_repos) >= options.count:
+                break
+
+        page += 1
+
+    write_jsonl(repos_path, accepted_repos)
+    if options.mode != "fresh":
+        seen_repo_ids.update(current_run_seen_repo_ids)
+        write_json(seen_index_path, sorted(seen_repo_ids))
+
+    manifest = {
+        "run_id": run_id,
+        "phase_name": "phase1_repository_sampling",
+        "command": "sample-repos",
+        "resolved_query": options.query,
+        "count_requested": options.count,
+        "count_collected": len(accepted_repos),
+        "per_page": options.per_page,
+        "mode": options.mode,
+        "page_count_scanned": max(page - 1, 0),
+        "github_total_count": total_count,
+        "output_files": {
+            "repos_jsonl": str(repos_path),
+            "seen_repo_ids_json": str(seen_index_path) if options.mode != "fresh" else None,
+        },
+        "sampled_at": utc_now(),
+    }
+    write_json(manifest_path, manifest)
+
+    return {
+        "run_id": run_id,
+        "count_collected": len(accepted_repos),
+        "repos_path": repos_path,
+        "manifest_path": manifest_path,
+        "seen_index_path": seen_index_path if options.mode != "fresh" else None,
+    }
+
+
+def normalize_repo_record(
+    repo: dict[str, Any],
+    run_id: str,
+    sample_query: str,
+    sample_page: int,
+    sampled_at: str,
+) -> dict[str, Any]:
+    return {
+        "run_id": run_id,
+        "repo_id": repo["id"],
+        "full_name": repo["full_name"],
+        "html_url": repo["html_url"],
+        "api_url": repo["url"],
+        "default_branch": repo.get("default_branch"),
+        "language": repo.get("language"),
+        "description": repo.get("description"),
+        "stargazers_count": repo.get("stargazers_count"),
+        "size_kb": repo.get("size"),
+        "fork": repo.get("fork"),
+        "archived": repo.get("archived"),
+        "visibility": repo.get("visibility"),
+        "sample_query": sample_query,
+        "sample_page": sample_page,
+        "sampled_at": sampled_at,
+    }
+
+
+def load_seen_repo_ids(path: Path) -> set[int]:
+    if not path.exists():
+        return set()
+    payload = read_json(path)
+    return {int(repo_id) for repo_id in payload}
diff --git a/src/github_datapipe/phases/phase2_commit_ingestion/__init__.py b/src/github_datapipe/phases/phase2_commit_ingestion/__init__.py
new file mode 100644
index 0000000..06b0858
--- /dev/null
+++ b/src/github_datapipe/phases/phase2_commit_ingestion/__init__.py
@@ -0,0 +1 @@
+"""Phase 2: commit history retrieval and persistence."""
diff --git a/src/github_datapipe/phases/phase2_commit_ingestion/service.py b/src/github_datapipe/phases/phase2_commit_ingestion/service.py
new file mode 100644
index 0000000..420a5c5
--- /dev/null
+++ b/src/github_datapipe/phases/phase2_commit_ingestion/service.py
@@ -0,0 +1,293 @@
+from __future__ import annotations
+
+from dataclasses import dataclass
+from pathlib import Path
+from typing import Any
+
+from github_datapipe.core.config import GithubConfig
+from github_datapipe.core.github_api import GithubApiClient, GithubApiError
+from github_datapipe.core.io import append_jsonl, read_json, read_jsonl, write_json, write_jsonl
+from github_datapipe.core.runtime import require_github_token, utc_now
+
+
+@dataclass(frozen=True)
+class FetchCommitsOptions:
+    output_root: Path = Path(GithubConfig.default_output_root)
+    run_id: str | None = None
+    repos_file: Path | None = None
+    mode: str = "refresh"
+    per_page: int = GithubConfig.default_per_page
+    max_pages_per_repo: int = GithubConfig.default_max_pages_per_repo
+    retry_count: int = GithubConfig.default_retry_count
+
+
+def fetch_commits(options: FetchCommitsOptions) -> dict[str, Any]:
+    token = require_github_token()
+    if options.max_pages_per_repo <= 0:
+        raise ValueError("`max_pages_per_repo` must be greater than 0.")
+    if options.per_page <= 0:
+        raise ValueError("`per_page` must be greater than 0.")
+
+    output_root = options.output_root.resolve()
+    repos_path, run_id = resolve_repo_input(options, output_root)
+
+    run_root = output_root / run_id
+    phase_root = run_root / "phase2_commit_ingestion"
+    commits_root = phase_root / "commits"
+    commits_path = commits_root / "commits-0001.jsonl"
+    status_path = phase_root / "repo_status.jsonl"
+    manifest_path = phase_root / "manifest.json"
+
+    repos = read_jsonl(repos_path)
+    if not repos:
+        raise ValueError(f"No repositories found in {repos_path}.")
+
+    prior_statuses = load_status_index(status_path) if options.mode == "resume" else {}
+
+    if options.mode == "refresh" and commits_path.exists():
+        commits_path.unlink()
+    status_rows: list[dict[str, Any]] = []
+    if options.mode == "resume":
+        status_rows.extend(read_jsonl(status_path))
+
+    processed_repositories = 0
+    completed_repositories = 0
+    warning_repositories = 0
+    failed_repositories = 0
+    written_commit_count = 0 if options.mode == "refresh" else count_jsonl_rows(commits_path)
+    client: GithubApiClient | None = None
+
+    for repo in repos:
+        repo_id = int(repo["repo_id"])
+        previous_status = prior_statuses.get(repo_id)
+        if options.mode == "resume" and previous_status == "complete":
+            continue
+
+        if client is None:
+            client = GithubApiClient(token=token)
+
+        processed_repositories += 1
+        status_record, commit_rows = process_repository(
+            client=client,
+            repo=repo,
+            run_id=run_id,
+            per_page=options.per_page,
+            max_pages_per_repo=options.max_pages_per_repo,
+            retry_count=options.retry_count,
+        )
+
+        status_rows.append(status_record)
+        written_commit_count += append_jsonl(commits_path, commit_rows)
+
+        if status_record["status"] == "complete":
+            completed_repositories += 1
+        elif status_record["status"] == "success_with_warning":
+            warning_repositories += 1
+        else:
+            failed_repositories += 1
+
+    write_jsonl(status_path, dedupe_status_rows(status_rows))
+
+    manifest = {
+        "run_id": run_id,
+        "phase_name": "phase2_commit_ingestion",
+        "command": "fetch-commits",
+        "mode": options.mode,
+        "per_page": options.per_page,
+        "max_pages_per_repo": options.max_pages_per_repo,
+        "retry_count": options.retry_count,
+        "processed_repositories": processed_repositories,
+        "completed_repositories": completed_repositories,
+        "warning_repositories": warning_repositories,
+        "failed_repositories": failed_repositories,
+        "written_commit_count": written_commit_count,
+        "input_files": {"repos_jsonl": str(repos_path)},
+        "output_files": {
+            "commits_jsonl": str(commits_path),
+            "repo_status_jsonl": str(status_path),
+        },
+        "fetched_at": utc_now(),
+    }
+    write_json(manifest_path, manifest)
+
+    return {
+        "run_id": run_id,
+        "processed_repositories": processed_repositories,
+        "completed_repositories": completed_repositories,
+        "warning_repositories": warning_repositories,
+        "failed_repositories": failed_repositories,
+        "commits_path": commits_path,
+        "status_path": status_path,
+        "manifest_path": manifest_path,
+    }
+
+
+def resolve_repo_input(options: FetchCommitsOptions, output_root: Path) -> tuple[Path, str]:
+    if options.run_id is not None:
+        return (
+            output_root / options.run_id / "phase1_repository_sampling" / "repos.jsonl",
+            options.run_id,
+        )
+
+    assert options.repos_file is not None
+    repos_path = options.repos_file.resolve()
+    repos = read_jsonl(repos_path)
+    if not repos:
+        raise ValueError(f"No repositories found in {repos_path}.")
+    return repos_path, str(repos[0]["run_id"])
+
+
+def process_repository(
+    client: GithubApiClient,
+    repo: dict[str, Any],
+    run_id: str,
+    per_page: int,
+    max_pages_per_repo: int,
+    retry_count: int,
+) -> tuple[dict[str, Any], list[dict[str, Any]]]:
+    full_name = repo["full_name"]
+    fetched_at = utc_now()
+
+    try:
+        repository = with_retries(
+            lambda: client.get_repository(full_name),
+            retry_count=retry_count,
+        )
+        branch = repository["default_branch"]
+        commit_rows: list[dict[str, Any]] = []
+        page = 1
+        last_page_size = 0
+
+        while page <= max_pages_per_repo:
+            commits = with_retries(
+                lambda page_number=page: client.list_commits(
+                    full_name=full_name,
+                    branch=branch,
+                    page=page_number,
+                    per_page=per_page,
+                ),
+                retry_count=retry_count,
+            )
+            if not commits:
+                break
+
+            last_page_size = len(commits)
+            commit_rows.extend(
+                normalize_commit_record(
+                    repo=repo,
+                    repository=repository,
+                    commit_payload=commit_payload,
+                    run_id=run_id,
+                    branch=branch,
+                    page_number=page,
+                    fetched_at=fetched_at,
+                )
+                for commit_payload in commits
+            )
+
+            if len(commits) < per_page:
+                break
+
+            page += 1
+
+        truncated = bool(commit_rows) and page > max_pages_per_repo and last_page_size == per_page
+        status = "success_with_warning" if truncated else "complete"
+        status_record = {
+            "run_id": run_id,
+            "repo_id": repo["repo_id"],
+            "repo_full_name": full_name,
+            "status": status,
+            "commit_count": len(commit_rows),
+            "default_branch_at_fetch": branch,
+            "truncated": truncated,
+            "truncation_reason": "max_pages" if truncated else None,
+            "failure_reason": None,
+            "fetched_at": fetched_at,
+        }
+        return status_record, commit_rows
+    except GithubApiError as exc:
+        status_record = {
+            "run_id": run_id,
+            "repo_id": repo["repo_id"],
+            "repo_full_name": full_name,
+            "status": "failed",
+            "commit_count": 0,
+            "default_branch_at_fetch": None,
+            "truncated": False,
+            "truncation_reason": None,
+            "failure_reason": str(exc),
+            "fetched_at": fetched_at,
+        }
+        return status_record, []
+
+
+def normalize_commit_record(
+    repo: dict[str, Any],
+    repository: dict[str, Any],
+    commit_payload: dict[str, Any],
+    run_id: str,
+    branch: str,
+    page_number: int,
+    fetched_at: str,
+) -> dict[str, Any]:
+    commit = commit_payload["commit"]
+    author = commit.get("author") or {}
+    committer = commit.get("committer") or {}
+    return {
+        "run_id": run_id,
+        "repo_id": repo["repo_id"],
+        "repo_full_name": repo["full_name"],
+        "repo_html_url": repo["html_url"],
+        "default_branch_at_fetch": branch,
+        "sha": commit_payload["sha"],
+        "commit_key": f"{repo['repo_id']}:{commit_payload['sha']}",
+        "parent_shas": [parent["sha"] for parent in commit_payload.get("parents", [])],
+        "author_name": author.get("name"),
+        "author_email": author.get("email"),
+        "author_date": author.get("date"),
+        "committer_name": committer.get("name"),
+        "committer_email": committer.get("email"),
+        "committer_date": committer.get("date"),
+        "message": commit.get("message"),
+        "html_url": commit_payload.get("html_url"),
+        "fetched_at": fetched_at,
+        "source_endpoint": f"/repos/{repository['full_name']}/commits",
+        "page_number": page_number,
+        "truncated": False,
+    }
+
+
+def with_retries(operation: Any, retry_count: int) -> Any:
+    last_error: Exception | None = None
+    for _ in range(retry_count + 1):
+        try:
+            return operation()
+        except GithubApiError as exc:
+            last_error = exc
+    assert last_error is not None
+    raise last_error
+
+
+def load_status_index(path: Path) -> dict[int, str]:
+    rows = read_jsonl(path)
+    latest_by_repo: dict[int, str] = {}
+    for row in rows:
+        latest_by_repo[int(row["repo_id"])] = row["status"]
+    return latest_by_repo
+
+
+def dedupe_status_rows(rows: list[dict[str, Any]]) -> list[dict[str, Any]]:
+    latest_by_repo: dict[int, dict[str, Any]] = {}
+    order: list[int] = []
+    for row in rows:
+        repo_id = int(row["repo_id"])
+        if repo_id not in latest_by_repo:
+            order.append(repo_id)
+        latest_by_repo[repo_id] = row
+    return [latest_by_repo[repo_id] for repo_id in order]
+
+
+def count_jsonl_rows(path: Path) -> int:
+    if not path.exists():
+        return 0
+    return len(path.read_text(encoding="utf-8").splitlines())
diff --git a/tests/test_phase1.py b/tests/test_phase1.py
index 7251cdd..90ddde3 100644
--- a/tests/test_phase1.py
+++ b/tests/test_phase1.py
@@ -5,8 +5,12 @@ from pathlib import Path
 
 import requests
 
-from github_datapipe.config import GithubConfig
-from github_datapipe.extract_repos import SampleReposOptions, resolve_query, sample_repositories
+from github_datapipe.core.config import GithubConfig
+from github_datapipe.phases.phase1_repository_sampling.service import (
+    SampleReposOptions,
+    resolve_query,
+    sample_repositories,
+)
 
 
 def test_resolve_query_uses_default_when_missing() -> None:
@@ -49,7 +53,7 @@ def test_sample_repositories_dedupes_and_persists(monkeypatch, tmp_path: Path) -
             return {"total_count": 3, "items": [fake_repo(102, "owner/repo-three")]}
 
     # Inject the mock sampler into the main code
-    monkeypatch.setattr("github_datapipe.extract_repos.GithubRepoSampler", FakeSampler)
+    monkeypatch.setattr("github_datapipe.phases.phase1_repository_sampling.service.GithubApiClient", FakeSampler)
 
     options = SampleReposOptions(
         count=3,
diff --git a/tests/test_phase2.py b/tests/test_phase2.py
new file mode 100644
index 0000000..9ee7fdb
--- /dev/null
+++ b/tests/test_phase2.py
@@ -0,0 +1,121 @@
+from __future__ import annotations
+
+import json
+from pathlib import Path
+
+import requests
+
+from github_datapipe.phases.phase2_commit_ingestion.service import (
+    FetchCommitsOptions,
+    fetch_commits,
+)
+
+
+def test_fetch_commits_writes_normalized_records_and_warning(monkeypatch, tmp_path: Path) -> None:
+    monkeypatch.setenv("github_token", "token")
+    repos_path = tmp_path / "run-test" / "phase1_repository_sampling" / "repos.jsonl"
+    repos_path.parent.mkdir(parents=True, exist_ok=True)
+    repos_path.write_text(json.dumps(fake_repo_record()) + "\n", encoding="utf-8")
+
+    class FakeClient:
+        def __init__(self, token: str, session: requests.Session | None = None) -> None:
+            self.token = token
+
+        def get_repository(self, full_name: str) -> dict:
+            return {"full_name": full_name, "default_branch": "main"}
+
+        def list_commits(self, full_name: str, branch: str, page: int, per_page: int) -> list[dict]:
+            if page == 1:
+                return [fake_commit_payload("a" * 40), fake_commit_payload("b" * 40)]
+            return []
+
+    monkeypatch.setattr("github_datapipe.phases.phase2_commit_ingestion.service.GithubApiClient", FakeClient)
+
+    result = fetch_commits(
+        FetchCommitsOptions(
+            output_root=tmp_path,
+            run_id="run-test",
+            mode="refresh",
+            per_page=2,
+            max_pages_per_repo=1,
+            retry_count=0,
+        )
+    )
+
+    commits_path = Path(result["commits_path"])
+    commit_rows = [json.loads(line) for line in commits_path.read_text(encoding="utf-8").splitlines()]
+    assert len(commit_rows) == 2
+    assert commit_rows[0]["commit_key"] == f"{fake_repo_record()['repo_id']}:{'a' * 40}"
+
+    status_path = Path(result["status_path"])
+    status_rows = [json.loads(line) for line in status_path.read_text(encoding="utf-8").splitlines()]
+    assert status_rows[0]["status"] == "success_with_warning"
+    assert status_rows[0]["truncated"] is True
+
+
+def test_fetch_commits_resume_skips_completed_repos(monkeypatch, tmp_path: Path) -> None:
+    monkeypatch.setenv("github_token", "token")
+    run_root = tmp_path / "run-test"
+    repos_path = run_root / "phase1_repository_sampling" / "repos.jsonl"
+    repos_path.parent.mkdir(parents=True, exist_ok=True)
+    repos_path.write_text(json.dumps(fake_repo_record()) + "\n", encoding="utf-8")
+
+    phase2_root = run_root / "phase2_commit_ingestion"
+    phase2_root.mkdir(parents=True, exist_ok=True)
+    (phase2_root / "repo_status.jsonl").write_text(
+        json.dumps(
+            {
+                "repo_id": fake_repo_record()["repo_id"],
+                "status": "complete",
+            }
+        )
+        + "\n",
+        encoding="utf-8",
+    )
+
+    class FakeClient:
+        def __init__(self, token: str, session: requests.Session | None = None) -> None:
+            raise AssertionError("Client should not be initialized for already completed repos")
+
+    monkeypatch.setattr("github_datapipe.phases.phase2_commit_ingestion.service.GithubApiClient", FakeClient)
+
+    result = fetch_commits(
+        FetchCommitsOptions(
+            output_root=tmp_path,
+            run_id="run-test",
+            mode="resume",
+            retry_count=0,
+        )
+    )
+
+    assert result["processed_repositories"] == 0
+
+
+def fake_repo_record() -> dict:
+    return {
+        "run_id": "run-test",
+        "repo_id": 100,
+        "full_name": "owner/repo-one",
+        "html_url": "https://github.com/owner/repo-one",
+    }
+
+
+def fake_commit_payload(sha: str) -> dict:
+    return {
+        "sha": sha,
+        "html_url": f"https://github.com/owner/repo-one/commit/{sha}",
+        "parents": [{"sha": "parent-sha"}],
+        "commit": {
+            "author": {
+                "name": "Alice",
+                "email": "alice@example.com",
+                "date": "2024-01-01T00:00:00Z",
+            },
+            "committer": {
+                "name": "Bob",
+                "email": "bob@example.com",
+                "date": "2024-01-01T00:00:00Z",
+            },
+            "message": "Initial commit",
+        },
+    }