diff --git a/src/codegen/cli/commands/config/main.py b/src/codegen/cli/commands/config/main.py
index 8905ab479..00d3143e4 100644
--- a/src/codegen/cli/commands/config/main.py
+++ b/src/codegen/cli/commands/config/main.py
@@ -5,8 +5,8 @@
 from rich.table import Table
 
 from codegen.configs.constants import ENV_FILENAME, GLOBAL_ENV_FILE
-from codegen.configs.session_manager import session_manager
 from codegen.configs.user_config import UserConfig
+from codegen.shared.path import get_git_root_path
 
 
 @click.group(name="config")
@@ -16,8 +16,7 @@ def config_command():
 
 
 @config_command.command(name="list")
-@click.option("--global", "is_global", is_flag=True, help="Lists the global configuration values")
-def list_command(is_global: bool):
+def list_command():
     """List current configuration values."""
 
     def flatten_dict(data: dict, prefix: str = "") -> dict:
@@ -33,7 +32,7 @@ def flatten_dict(data: dict, prefix: str = "") -> dict:
                 items[full_key] = value
         return items
 
-    config = _get_user_config(is_global)
+    config = _get_user_config()
     flat_config = flatten_dict(config.to_dict())
     sorted_items = sorted(flat_config.items(), key=lambda x: x[0])
 
@@ -82,10 +81,9 @@ def flatten_dict(data: dict, prefix: str = "") -> dict:
 
 @config_command.command(name="get")
 @click.argument("key")
-@click.option("--global", "is_global", is_flag=True, help="Get the global configuration value")
-def get_command(key: str, is_global: bool):
+def get_command(key: str):
     """Get a configuration value."""
-    config = _get_user_config(is_global)
+    config = _get_user_config()
     if not config.has_key(key):
         rich.print(f"[red]Error: Configuration key '{key}' not found[/red]")
         return
@@ -98,10 +96,9 @@ def get_command(key: str, is_global: bool):
 @config_command.command(name="set")
 @click.argument("key")
 @click.argument("value")
-@click.option("--global", "is_global", is_flag=True, help="Sets the global configuration value")
-def set_command(key: str, value: str, is_global: bool):
+def set_command(key: str, value: str):
     """Set a configuration value and write to .env"""
-    config = _get_user_config(is_global)
+    config = _get_user_config()
     if not config.has_key(key):
         rich.print(f"[red]Error: Configuration key '{key}' not found[/red]")
         return
@@ -118,10 +115,10 @@ def set_command(key: str, value: str, is_global: bool):
     rich.print(f"[green]Successfully set {key}=[magenta]{value}[/magenta] and saved to {ENV_FILENAME}[/green]")
 
 
-def _get_user_config(is_global: bool) -> UserConfig:
-    if is_global or (active_session_path := session_manager.get_active_session()) is None:
+def _get_user_config() -> UserConfig:
+    if (project_root := get_git_root_path()) is None:
         env_filepath = GLOBAL_ENV_FILE
     else:
-        env_filepath = active_session_path / ENV_FILENAME
+        env_filepath = project_root / ENV_FILENAME
 
     return UserConfig(env_filepath)
diff --git a/src/codegen/cli/commands/init/main.py b/src/codegen/cli/commands/init/main.py
index e85de1c4e..b10d6ca23 100644
--- a/src/codegen/cli/commands/init/main.py
+++ b/src/codegen/cli/commands/init/main.py
@@ -8,7 +8,7 @@
 from codegen.cli.commands.init.render import get_success_message
 from codegen.cli.rich.codeblocks import format_command
 from codegen.cli.workspace.initialize_workspace import initialize_codegen
-from codegen.git.utils.path import get_git_root_path
+from codegen.shared.path import get_git_root_path
 
 
 @click.command(name="init")
diff --git a/src/codegen/cli/env/global_env.py b/src/codegen/cli/env/global_env.py
index 51c3772d1..57eaa02a7 100644
--- a/src/codegen/cli/env/global_env.py
+++ b/src/codegen/cli/env/global_env.py
@@ -38,20 +38,24 @@ def _parse_env(self) -> Environment:
     def _load_dotenv(self) -> None:
         env_file = find_dotenv(filename=f".env.{self.ENV}")
         # if env specific .env file does not exist, try to load .env
-        load_dotenv(env_file or None)
+        load_dotenv(env_file or None, override=True)
 
     def _get_env_var(self, var_name, required: bool = False) -> str:
         if self.ENV == "local":
             return ""
 
-        value = os.environ.get(var_name)
-        if value:
+        if value := os.environ.get(var_name):
             return value
+
         if required:
             msg = f"Environment variable {var_name} is not set with ENV={self.ENV}!"
             raise ValueError(msg)
         return ""
 
+    def __repr__(self) -> str:
+        # Returns all env vars in a readable format
+        return "\n".join([f"{k}={v}" for k, v in self.__dict__.items()])
+
 
 # NOTE: load and store envvars once
 global_env = GlobalEnv()
diff --git a/src/codegen/configs/models/base_config.py b/src/codegen/configs/models/base_config.py
index 4bbd25a84..3a82223de 100644
--- a/src/codegen/configs/models/base_config.py
+++ b/src/codegen/configs/models/base_config.py
@@ -1,11 +1,11 @@
 from abc import ABC
 from pathlib import Path
 
-from dotenv import set_key
+from dotenv import load_dotenv, set_key
 from pydantic_settings import BaseSettings, SettingsConfigDict
 
 from codegen.configs.constants import ENV_FILENAME, GLOBAL_ENV_FILE
-from codegen.configs.session_manager import session_root
+from codegen.shared.path import get_git_root_path
 
 
 class BaseConfig(BaseSettings, ABC):
@@ -18,20 +18,18 @@ class BaseConfig(BaseSettings, ABC):
 
     def __init__(self, prefix: str, env_filepath: Path | None = None, *args, **kwargs) -> None:
         if env_filepath is None:
-            root_path = session_root
+            root_path = get_git_root_path()
             if root_path is not None:
                 env_filepath = root_path / ENV_FILENAME
 
         # Only include env files that exist
-        env_filepaths = []
         if GLOBAL_ENV_FILE.exists():
-            env_filepaths.append(GLOBAL_ENV_FILE)
+            load_dotenv(GLOBAL_ENV_FILE, override=True)
+
         if env_filepath and env_filepath.exists() and env_filepath != GLOBAL_ENV_FILE:
-            env_filepaths.append(env_filepath)
+            load_dotenv(env_filepath, override=True)
 
         self.model_config["env_prefix"] = f"{prefix.upper()}_" if len(prefix) > 0 else ""
-        self.model_config["env_file"] = env_filepaths
-
         super().__init__(*args, **kwargs)
 
     @property
diff --git a/src/codegen/configs/models/repository.py b/src/codegen/configs/models/repository.py
index c75f1dd9f..d4960c503 100644
--- a/src/codegen/configs/models/repository.py
+++ b/src/codegen/configs/models/repository.py
@@ -37,6 +37,3 @@ def full_name(self) -> str | None:
         if self.owner is not None:
             return f"{self.owner}/{self.name}"
         return None
-
-
-DefaultRepoConfig = RepositoryConfig()
diff --git a/src/codegen/configs/models/secrets.py b/src/codegen/configs/models/secrets.py
index d0e9e3a77..208999ebe 100644
--- a/src/codegen/configs/models/secrets.py
+++ b/src/codegen/configs/models/secrets.py
@@ -14,6 +14,3 @@ def __init__(self, prefix: str = "", *args, **kwargs) -> None:
     github_token: str | None = None
     openai_api_key: str | None = None
     linear_api_key: str | None = None
-
-
-DefaultSecrets = SecretsConfig()
diff --git a/src/codegen/configs/session_manager.py b/src/codegen/configs/session_manager.py
index c8c48cfe7..f69a9b479 100644
--- a/src/codegen/configs/session_manager.py
+++ b/src/codegen/configs/session_manager.py
@@ -3,7 +3,7 @@
 import json
 from pathlib import Path
 
-from codegen.configs.constants import CODEGEN_DIR_NAME, SESSION_FILE
+from codegen.configs.constants import SESSION_FILE
 
 
 class SessionManager:
@@ -61,34 +61,4 @@ def __str__(self) -> str:
         return f"GlobalConfig:\n  Active Session: {active}\n  Sessions:\n    {sessions_str}\n  Global Session:\n    {self.session_config}"
 
 
-def _get_project_root() -> Path | None:
-    """Get the active codegen directory."""
-    active_session = session_manager.get_active_session()
-    if active_session:
-        return active_session
-
-    try:
-        path = Path.cwd().resolve()
-    except FileNotFoundError:
-        # Current directory is not accessible
-        return None
-
-    while True:
-        codegen_path = path / CODEGEN_DIR_NAME
-        git_path = path / ".git"
-
-        if codegen_path.exists():
-            return path
-        if git_path.exists():
-            return path
-
-        parent = path.parent.resolve()
-        if parent == path:  # We've reached the root directory
-            break
-        path = parent
-
-    return None
-
-
 session_manager = SessionManager()
-session_root = _get_project_root()
diff --git a/src/codegen/configs/user_config.py b/src/codegen/configs/user_config.py
index 511929ad9..ecebec4d1 100644
--- a/src/codegen/configs/user_config.py
+++ b/src/codegen/configs/user_config.py
@@ -34,13 +34,13 @@ def to_dict(self) -> dict:
         for key, value in self.repository.model_dump().items():
             config_dict[f"{self.repository.env_prefix}{key}".upper()] = value
 
-        # Add secrets configs with 'secrets_' prefix
-        for key, value in self.secrets.model_dump().items():
-            config_dict[f"{self.secrets.env_prefix}{key}".upper()] = value
-
         # Add feature flags configs with 'feature_flags_' prefix
         for key, value in self.codebase.model_dump().items():
             config_dict[f"{self.codebase.env_prefix}{key}".upper()] = value
+
+        # Add secrets configs
+        for key, value in self.secrets.model_dump().items():
+            config_dict[f"{self.secrets.env_prefix}{key}".upper()] = value
         return config_dict
 
     def has_key(self, full_key: str) -> bool:
diff --git a/src/codegen/extensions/lsp/protocol.py b/src/codegen/extensions/lsp/protocol.py
index 2aedd4795..cc0d55c29 100644
--- a/src/codegen/extensions/lsp/protocol.py
+++ b/src/codegen/extensions/lsp/protocol.py
@@ -5,7 +5,7 @@
 from lsprotocol.types import INITIALIZE, InitializeParams, InitializeResult
 from pygls.protocol import LanguageServerProtocol, lsp_method
 
-from codegen.configs.models.codebase import DefaultCodebaseConfig
+from codegen.configs.models.codebase import CodebaseConfig
 from codegen.extensions.lsp.io import LSPIO
 from codegen.extensions.lsp.progress import LSPProgress
 from codegen.extensions.lsp.utils import get_path
@@ -26,7 +26,7 @@ def _init_codebase(self, params: InitializeParams) -> None:
             root = get_path(params.root_uri)
         else:
             root = os.getcwd()
-        config = DefaultCodebaseConfig.model_copy(update={"full_range_index": True})
+        config = CodebaseConfig().model_copy(update={"full_range_index": True})
         io = LSPIO(self.workspace)
         self._server.codebase = Codebase(repo_path=str(root), config=config, io=io, progress=progress)
         self._server.progress_manager = progress
diff --git a/src/codegen/git/clients/git_repo_client.py b/src/codegen/git/clients/git_repo_client.py
index 73a3cffed..dee994f7a 100644
--- a/src/codegen/git/clients/git_repo_client.py
+++ b/src/codegen/git/clients/git_repo_client.py
@@ -15,6 +15,7 @@
 from github.Tag import Tag
 from github.Workflow import Workflow
 
+from codegen.configs.models.secrets import SecretsConfig
 from codegen.git.clients.github_client import GithubClient
 from codegen.git.schemas.repo_config import RepoConfig
 from codegen.git.utils.format import format_comparison
@@ -29,9 +30,9 @@ class GitRepoClient:
     gh_client: GithubClient
     _repo: Repository
 
-    def __init__(self, repo_config: RepoConfig, access_token: str) -> None:
+    def __init__(self, repo_config: RepoConfig, access_token: str | None = None) -> None:
         self.repo_config = repo_config
-        self.gh_client = self._create_github_client(token=access_token)
+        self.gh_client = self._create_github_client(token=access_token or SecretsConfig().github_token)
         self._repo = self._create_client()
 
     def _create_github_client(self, token: str) -> GithubClient:
diff --git a/src/codegen/git/repo_operator/repo_operator.py b/src/codegen/git/repo_operator/repo_operator.py
index 63ff3ca3f..eb765502b 100644
--- a/src/codegen/git/repo_operator/repo_operator.py
+++ b/src/codegen/git/repo_operator/repo_operator.py
@@ -17,7 +17,7 @@
 from github.IssueComment import IssueComment
 from github.PullRequest import PullRequest
 
-from codegen.configs.models.secrets import DefaultSecrets
+from codegen.configs.models.secrets import SecretsConfig
 from codegen.git.clients.git_repo_client import GitRepoClient
 from codegen.git.configs.constants import CODEGEN_BOT_EMAIL, CODEGEN_BOT_NAME
 from codegen.git.repo_operator.local_git_repo import LocalGitRepo
@@ -58,7 +58,7 @@ def __init__(
     ) -> None:
         assert repo_config is not None
         self.repo_config = repo_config
-        self.access_token = access_token or DefaultSecrets.github_token
+        self.access_token = access_token or SecretsConfig().github_token
         self.base_dir = repo_config.base_dir
         self.bot_commit = bot_commit
 
@@ -839,7 +839,7 @@ def create_from_repo(cls, repo_path: str, url: str, access_token: str | None = N
             url (str): Git URL of the repository
             access_token (str | None): Optional GitHub API key for operations that need GitHub access
         """
-        access_token = access_token or DefaultSecrets.github_token
+        access_token = access_token or SecretsConfig().github_token
         if access_token:
             url = add_access_token_to_url(url=url, token=access_token)
 
diff --git a/src/codegen/runner/clients/codebase_client.py b/src/codegen/runner/clients/codebase_client.py
index 5f0e56a83..5cbcdb992 100644
--- a/src/codegen/runner/clients/codebase_client.py
+++ b/src/codegen/runner/clients/codebase_client.py
@@ -2,7 +2,7 @@
 
 import logging
 
-from codegen.configs.models import secrets
+from codegen.configs.models.secrets import SecretsConfig
 from codegen.git.schemas.repo_config import RepoConfig
 from codegen.runner.clients.server_client import LocalServerClient
 from codegen.runner.models.apis import SANDBOX_SERVER_PORT
@@ -16,11 +16,9 @@ class CodebaseClient(LocalServerClient):
     """Client for interacting with the locally hosted sandbox server."""
 
     repo_config: RepoConfig
-    git_access_token: str | None
 
-    def __init__(self, repo_config: RepoConfig, git_access_token: str | None, host: str = "127.0.0.1", port: int = SANDBOX_SERVER_PORT):
+    def __init__(self, repo_config: RepoConfig, host: str = "127.0.0.1", port: int = SANDBOX_SERVER_PORT):
         self.repo_config = repo_config
-        self.git_access_token = git_access_token
         super().__init__(server_path=RUNNER_SERVER_PATH, host=host, port=port)
 
     def _get_envs(self) -> dict:
@@ -29,9 +27,8 @@ def _get_envs(self) -> dict:
             "REPOSITORY_LANGUAGE": self.repo_config.language.value,
             "REPOSITORY_OWNER": self.repo_config.organization_name,
             "REPOSITORY_PATH": str(self.repo_config.repo_path),
+            "GITHUB_TOKEN": SecretsConfig().github_token,
         }
-        if self.git_access_token is not None:
-            codebase_envs["GITHUB_TOKEN"] = self.git_access_token
 
         envs.update(codebase_envs)
         return envs
@@ -40,5 +37,5 @@ def _get_envs(self) -> dict:
 if __name__ == "__main__":
     test_config = RepoConfig.from_repo_path("/Users/caroljung/git/codegen/codegen-agi")
     test_config.full_name = "codegen-sh/codegen-agi"
-    client = CodebaseClient(test_config, secrets.github_token)
+    client = CodebaseClient(test_config)
     print(client.healthcheck())
diff --git a/src/codegen/runner/sandbox/runner.py b/src/codegen/runner/sandbox/runner.py
index 1e9c4f9dc..bd6eb5159 100644
--- a/src/codegen/runner/sandbox/runner.py
+++ b/src/codegen/runner/sandbox/runner.py
@@ -29,9 +29,9 @@ class SandboxRunner:
     codebase: CodebaseType
     executor: SandboxExecutor
 
-    def __init__(self, repo_config: RepoConfig, access_token: str) -> None:
+    def __init__(self, repo_config: RepoConfig) -> None:
         self.repo = repo_config
-        self.op = RepoOperator(repo_config=self.repo, access_token=access_token, setup_option=SetupOption.PULL_OR_CLONE)
+        self.op = RepoOperator(repo_config=self.repo, setup_option=SetupOption.PULL_OR_CLONE)
         self.commit = self.op.git_cli.head.commit
 
     async def warmup(self) -> None:
diff --git a/src/codegen/runner/sandbox/server.py b/src/codegen/runner/sandbox/server.py
index 35689f2c1..52b42cb99 100644
--- a/src/codegen/runner/sandbox/server.py
+++ b/src/codegen/runner/sandbox/server.py
@@ -7,8 +7,7 @@
 import psutil
 from fastapi import FastAPI
 
-from codegen.configs.models.repository import DefaultRepoConfig
-from codegen.configs.models.secrets import DefaultSecrets
+from codegen.configs.models.repository import RepositoryConfig
 from codegen.git.schemas.repo_config import RepoConfig
 from codegen.runner.enums.warmup_state import WarmupState
 from codegen.runner.models.apis import (
@@ -40,15 +39,16 @@ async def lifespan(server: FastAPI):
     global runner
 
     try:
-        server_info = ServerInfo(repo_name=DefaultRepoConfig.full_name or DefaultRepoConfig.name)
+        default_repo_config = RepositoryConfig()
+        server_info = ServerInfo(repo_name=default_repo_config.full_name or default_repo_config.name)
         logger.info(f"Starting up sandbox fastapi server for repo_name={server_info.repo_name}")
         repo_config = RepoConfig(
-            name=DefaultRepoConfig.name,
-            full_name=DefaultRepoConfig.full_name,
-            base_dir=os.path.dirname(DefaultRepoConfig.path),
-            language=ProgrammingLanguage(DefaultRepoConfig.language.upper()),
+            name=default_repo_config.name,
+            full_name=default_repo_config.full_name,
+            base_dir=os.path.dirname(default_repo_config.path),
+            language=ProgrammingLanguage(default_repo_config.language.upper()),
         )
-        runner = SandboxRunner(repo_config=repo_config, access_token=DefaultSecrets.github_token)
+        runner = SandboxRunner(repo_config=repo_config)
         server_info.warmup_state = WarmupState.PENDING
         await runner.warmup()
         server_info.warmup_state = WarmupState.COMPLETED
diff --git a/src/codegen/sdk/code_generation/codegen_sdk_codebase.py b/src/codegen/sdk/code_generation/codegen_sdk_codebase.py
index 36d012718..d6ede5175 100644
--- a/src/codegen/sdk/code_generation/codegen_sdk_codebase.py
+++ b/src/codegen/sdk/code_generation/codegen_sdk_codebase.py
@@ -1,6 +1,5 @@
 import os.path
 
-from codegen.configs.models.codebase import DefaultCodebaseConfig
 from codegen.sdk.code_generation.current_code_codebase import get_codegen_codebase_base_path, get_current_code_codebase
 from codegen.sdk.core.codebase import Codebase
 
@@ -12,5 +11,5 @@ def get_codegen_sdk_subdirectories() -> list[str]:
 
 def get_codegen_sdk_codebase() -> Codebase:
     """Grabs a Codebase w/ GraphSitter content. Responsible for figuring out where it is, e.g. in Modal or local"""
-    codebase = get_current_code_codebase(DefaultCodebaseConfig, subdirectories=get_codegen_sdk_subdirectories())
+    codebase = get_current_code_codebase(subdirectories=get_codegen_sdk_subdirectories())
     return codebase
diff --git a/src/codegen/sdk/code_generation/current_code_codebase.py b/src/codegen/sdk/code_generation/current_code_codebase.py
index 5c097c09d..3cab53df2 100644
--- a/src/codegen/sdk/code_generation/current_code_codebase.py
+++ b/src/codegen/sdk/code_generation/current_code_codebase.py
@@ -4,8 +4,8 @@
 from pathlib import Path
 from typing import TypedDict
 
-from codegen.configs.models.codebase import CodebaseConfig, DefaultCodebaseConfig
-from codegen.configs.models.secrets import DefaultSecrets, SecretsConfig
+from codegen.configs.models.codebase import CodebaseConfig
+from codegen.configs.models.secrets import SecretsConfig
 from codegen.git.repo_operator.repo_operator import RepoOperator
 from codegen.git.schemas.repo_config import RepoConfig
 from codegen.sdk.codebase.config import ProjectConfig
@@ -34,7 +34,7 @@ def get_codegen_codebase_base_path() -> str:
     return "src" if "src" in codegen_base_dir else ""
 
 
-def get_current_code_codebase(config: CodebaseConfig = DefaultCodebaseConfig, secrets: SecretsConfig = DefaultSecrets, subdirectories: list[str] | None = None) -> CodebaseType:
+def get_current_code_codebase(config: CodebaseConfig | None = None, secrets: SecretsConfig | None = None, subdirectories: list[str] | None = None) -> CodebaseType:
     """Returns a Codebase for the code that is *currently running* (i.e. the Codegen repo)"""
     codegen_repo_path = get_graphsitter_repo_path()
     base_dir = get_codegen_codebase_base_path()
@@ -44,7 +44,7 @@ def get_current_code_codebase(config: CodebaseConfig = DefaultCodebaseConfig, se
     repo_config.respect_gitignore = False
     op = RepoOperator(repo_config=repo_config, bot_commit=False)
 
-    config = config.model_copy(update={"base_path": base_dir})
+    config = (config or CodebaseConfig()).model_copy(update={"base_path": base_dir})
     projects = [ProjectConfig(repo_operator=op, programming_language=ProgrammingLanguage.PYTHON, subdirectories=subdirectories, base_path=base_dir)]
     codebase = Codebase(projects=projects, config=config, secrets=secrets)
     return codebase
diff --git a/src/codegen/sdk/codebase/codebase_context.py b/src/codegen/sdk/codebase/codebase_context.py
index f915217ba..62a24eb16 100644
--- a/src/codegen/sdk/codebase/codebase_context.py
+++ b/src/codegen/sdk/codebase/codebase_context.py
@@ -11,8 +11,8 @@
 
 from rustworkx import PyDiGraph, WeightedEdgeList
 
-from codegen.configs.models.codebase import DefaultCodebaseConfig
-from codegen.configs.models.secrets import DefaultSecrets, SecretsConfig
+from codegen.configs.models.codebase import CodebaseConfig
+from codegen.configs.models.secrets import SecretsConfig
 from codegen.sdk.codebase.config import ProjectConfig, SessionOptions
 from codegen.sdk.codebase.config_parser import ConfigParser, get_config_parser_for_language
 from codegen.sdk.codebase.diff_lite import ChangeType, DiffLite
@@ -39,7 +39,6 @@
     from codeowners import CodeOwners as CodeOwnersParser
     from git import Commit as GitCommit
 
-    from codegen.configs.models.codebase import CodebaseConfig
     from codegen.git.repo_operator.repo_operator import RepoOperator
     from codegen.sdk.codebase.io.io import IO
     from codegen.sdk.codebase.node_classes.node_classes import NodeClasses
@@ -134,8 +133,8 @@ class CodebaseContext:
     def __init__(
         self,
         projects: list[ProjectConfig],
-        config: CodebaseConfig = DefaultCodebaseConfig,
-        secrets: SecretsConfig = DefaultSecrets,
+        config: CodebaseConfig | None = None,
+        secrets: SecretsConfig | None = None,
         io: IO | None = None,
         progress: Progress | None = None,
     ) -> None:
@@ -161,8 +160,8 @@ def __init__(
         self.io = io or FileIO()
         context = projects[0]
         self.node_classes = get_node_classes(context.programming_language)
-        self.config = config
-        self.secrets = secrets
+        self.config = config or CodebaseConfig()
+        self.secrets = secrets or SecretsConfig()
         self.repo_name = context.repo_operator.repo_name
         self.repo_path = str(Path(context.repo_operator.repo_path).resolve())
         self.full_path = os.path.join(self.repo_path, context.base_path) if context.base_path else self.repo_path
@@ -174,7 +173,7 @@ def __init__(
         self.init_nodes = None
         self.init_edges = None
         self.directories = dict()
-        self.parser = Parser.from_node_classes(self.node_classes, log_parse_warnings=config.debug)
+        self.parser = Parser.from_node_classes(self.node_classes, log_parse_warnings=self.config.debug)
         self.extensions = self.node_classes.file_cls.get_extensions()
         # ORDER IS IMPORTANT HERE!
         self.config_parser = get_config_parser_for_language(context.programming_language, self)
diff --git a/src/codegen/sdk/codebase/factory/codebase_factory.py b/src/codegen/sdk/codebase/factory/codebase_factory.py
index f122cc371..009992311 100644
--- a/src/codegen/sdk/codebase/factory/codebase_factory.py
+++ b/src/codegen/sdk/codebase/factory/codebase_factory.py
@@ -1,7 +1,7 @@
 from codegen.configs.models.codebase import CodebaseConfig
-from codegen.configs.models.secrets import DefaultSecrets, SecretsConfig
+from codegen.configs.models.secrets import SecretsConfig
 from codegen.git.repo_operator.repo_operator import RepoOperator
-from codegen.sdk.codebase.config import DefaultCodebaseConfig, ProjectConfig
+from codegen.sdk.codebase.config import ProjectConfig
 from codegen.sdk.core.codebase import (
     Codebase,
     CodebaseType,
@@ -20,8 +20,8 @@ def get_codebase_from_files(
         files: dict[str, str] = {},
         bot_commit: bool = True,
         programming_language: ProgrammingLanguage = ProgrammingLanguage.PYTHON,
-        config: CodebaseConfig = DefaultCodebaseConfig,
-        secrets: SecretsConfig = DefaultSecrets,
+        config: CodebaseConfig | None = None,
+        secrets: SecretsConfig | None = None,
     ) -> CodebaseType:
         op = RepoOperator.create_from_files(repo_path=repo_path, files=files, bot_commit=bot_commit)
         projects = [ProjectConfig(repo_operator=op, programming_language=programming_language)]
diff --git a/src/codegen/sdk/codebase/factory/get_session.py b/src/codegen/sdk/codebase/factory/get_session.py
index cb0d4df33..189eec6e6 100644
--- a/src/codegen/sdk/codebase/factory/get_session.py
+++ b/src/codegen/sdk/codebase/factory/get_session.py
@@ -5,7 +5,7 @@
 from typing import Literal, overload
 
 from codegen.configs.models.codebase import CodebaseConfig
-from codegen.configs.models.secrets import DefaultSecrets, SecretsConfig
+from codegen.configs.models.secrets import SecretsConfig
 from codegen.git.repo_operator.repo_operator import RepoOperator
 from codegen.sdk.codebase.codebase_context import CodebaseContext
 from codegen.sdk.codebase.config import ProjectConfig, SessionOptions, TestFlags
@@ -27,7 +27,7 @@ def get_codebase_session(
     verify_output: bool = True,
     config: CodebaseConfig = TestFlags,
     session_options: SessionOptions = SessionOptions(),
-    secrets: SecretsConfig = DefaultSecrets,
+    secrets: SecretsConfig | None = None,
 ) -> AbstractContextManager[PyCodebaseType]: ...
 
 
@@ -42,7 +42,7 @@ def get_codebase_session(
     verify_output: bool = True,
     config: CodebaseConfig = TestFlags,
     session_options: SessionOptions = SessionOptions(),
-    secrets: SecretsConfig = DefaultSecrets,
+    secrets: SecretsConfig | None = None,
 ) -> AbstractContextManager[PyCodebaseType]: ...
 
 
@@ -57,7 +57,7 @@ def get_codebase_session(
     verify_output: bool = True,
     config: CodebaseConfig = TestFlags,
     session_options: SessionOptions = SessionOptions(),
-    secrets: SecretsConfig = DefaultSecrets,
+    secrets: SecretsConfig | None = None,
 ) -> AbstractContextManager[TSCodebaseType]: ...
 
 
@@ -72,7 +72,7 @@ def get_codebase_session(
     verify_output: bool = True,
     config: CodebaseConfig = TestFlags,
     session_options: SessionOptions = SessionOptions(),
-    secrets: SecretsConfig = DefaultSecrets,
+    secrets: SecretsConfig | None = None,
 ) -> Generator[Codebase, None, None]:
     """Gives you a Codebase operating on the files you provided as a dict"""
     codebase = CodebaseFactory.get_codebase_from_files(repo_path=str(tmpdir), files=files, config=config, secrets=secrets, programming_language=programming_language)
diff --git a/src/codegen/sdk/core/codebase.py b/src/codegen/sdk/core/codebase.py
index 6858462f5..090e87c50 100644
--- a/src/codegen/sdk/core/codebase.py
+++ b/src/codegen/sdk/core/codebase.py
@@ -22,8 +22,8 @@
 from rich.console import Console
 from typing_extensions import TypeVar, deprecated
 
-from codegen.configs.models.codebase import CodebaseConfig, DefaultCodebaseConfig
-from codegen.configs.models.secrets import DefaultSecrets, SecretsConfig
+from codegen.configs.models.codebase import CodebaseConfig
+from codegen.configs.models.secrets import SecretsConfig
 from codegen.git.repo_operator.repo_operator import RepoOperator
 from codegen.git.schemas.enums import CheckoutResult
 from codegen.git.utils.pr_review import CodegenPR
@@ -130,8 +130,8 @@ def __init__(
         *,
         language: None = None,
         projects: list[ProjectConfig] | ProjectConfig,
-        config: CodebaseConfig = DefaultCodebaseConfig,
-        secrets: SecretsConfig = DefaultSecrets,
+        config: CodebaseConfig | None = None,
+        secrets: SecretsConfig | None = None,
         io: IO | None = None,
         progress: Progress | None = None,
     ) -> None: ...
@@ -143,8 +143,8 @@ def __init__(
         *,
         language: Literal["python", "typescript"] | ProgrammingLanguage | None = None,
         projects: None = None,
-        config: CodebaseConfig = DefaultCodebaseConfig,
-        secrets: SecretsConfig = DefaultSecrets,
+        config: CodebaseConfig | None = None,
+        secrets: SecretsConfig | None = None,
         io: IO | None = None,
         progress: Progress | None = None,
     ) -> None: ...
@@ -155,8 +155,8 @@ def __init__(
         *,
         language: Literal["python", "typescript"] | ProgrammingLanguage | None = None,
         projects: list[ProjectConfig] | ProjectConfig | None = None,
-        config: CodebaseConfig = DefaultCodebaseConfig,
-        secrets: SecretsConfig = DefaultSecrets,
+        config: CodebaseConfig | None = None,
+        secrets: SecretsConfig | None = None,
         io: IO | None = None,
         progress: Progress | None = None,
     ) -> None:
@@ -1257,8 +1257,8 @@ def from_repo(
         tmp_dir: str | None = "/tmp/codegen",
         commit: str | None = None,
         language: Literal["python", "typescript"] | ProgrammingLanguage | None = None,
-        config: CodebaseConfig = DefaultCodebaseConfig,
-        secrets: SecretsConfig = DefaultSecrets,
+        config: CodebaseConfig | None = None,
+        secrets: SecretsConfig | None = None,
     ) -> "Codebase":
         """Fetches a codebase from GitHub and returns a Codebase instance.
 
@@ -1268,8 +1268,8 @@ def from_repo(
             commit (Optional[str]): The specific commit hash to clone. Defaults to HEAD
             shallow (bool): Whether to do a shallow clone. Defaults to True
             language (Literal["python", "typescript"] | ProgrammingLanguage | None): The programming language of the repo. Defaults to None.
-            config (CodebaseConfig): Configuration for the codebase. Defaults to pre-defined defaults.
-            secrets (SecretsConfig): Configuration for the secrets. Defaults to empty values.
+            config (CodebaseConfig): Configuration for the codebase. Defaults to pre-defined defaults if None.
+            secrets (SecretsConfig): Configuration for the secrets. Defaults to empty values if None.
 
         Returns:
             Codebase: A Codebase instance initialized with the cloned repository
@@ -1295,10 +1295,10 @@ def from_repo(
             # Use RepoOperator to fetch the repository
             logger.info("Cloning repository...")
             if commit is None:
-                repo_operator = RepoOperator.create_from_repo(repo_path=repo_path, url=repo_url, access_token=secrets.github_token)
+                repo_operator = RepoOperator.create_from_repo(repo_path=repo_path, url=repo_url)
             else:
                 # Ensure the operator can handle remote operations
-                repo_operator = RepoOperator.create_from_commit(repo_path=repo_path, commit=commit, url=repo_url, access_token=secrets.github_token)
+                repo_operator = RepoOperator.create_from_commit(repo_path=repo_path, commit=commit, url=repo_url)
             logger.info("Clone completed successfully")
 
             # Initialize and return codebase with proper context
diff --git a/src/codegen/git/utils/path.py b/src/codegen/shared/path.py
similarity index 76%
rename from src/codegen/git/utils/path.py
rename to src/codegen/shared/path.py
index c4cd063f8..a541c42cd 100644
--- a/src/codegen/git/utils/path.py
+++ b/src/codegen/shared/path.py
@@ -3,9 +3,11 @@
 from pathlib import Path
 
 
-def get_git_root_path(path: Path) -> Path | None:
+def get_git_root_path(path: Path | None = None) -> Path | None:
     """Get the closest root of the git repository containing the given path"""
     try:
+        path = path or Path.cwd()
+        path = path.resolve()
         os.chdir(path)
         output = subprocess.run(["git", "rev-parse", "--show-toplevel"], capture_output=True, check=True, text=True)
         return Path(output.stdout.strip())
diff --git a/tests/integration/codegen/runner/conftest.py b/tests/integration/codegen/runner/conftest.py
index 1c4bf52b7..7180568b3 100644
--- a/tests/integration/codegen/runner/conftest.py
+++ b/tests/integration/codegen/runner/conftest.py
@@ -5,7 +5,6 @@
 
 import pytest
 
-from codegen.configs.models.secrets import DefaultSecrets
 from codegen.git.clients.git_repo_client import GitRepoClient
 from codegen.git.repo_operator.repo_operator import RepoOperator
 from codegen.git.schemas.enums import SetupOption
@@ -36,16 +35,16 @@ def repo_config(tmpdir) -> Generator[RepoConfig, None, None]:
 
 @pytest.fixture
 def op(repo_config: RepoConfig) -> Generator[RepoOperator, None, None]:
-    yield RepoOperator(repo_config=repo_config, access_token=DefaultSecrets.github_token, setup_option=SetupOption.PULL_OR_CLONE)
+    yield RepoOperator(repo_config=repo_config, setup_option=SetupOption.PULL_OR_CLONE)
 
 
 @pytest.fixture
-def git_repo_client(repo_config: RepoConfig) -> Generator[GitRepoClient, None, None]:
-    yield GitRepoClient(repo_config=repo_config, access_token=DefaultSecrets.github_token)
+def git_repo_client(op: RepoOperator, repo_config: RepoConfig) -> Generator[GitRepoClient, None, None]:
+    yield GitRepoClient(repo_config=repo_config, access_token=op.access_token)
 
 
 @pytest.fixture
 def codebase_client(repo_config: RepoConfig, get_free_port) -> Generator[CodebaseClient, None, None]:
-    sb_client = CodebaseClient(repo_config=repo_config, port=get_free_port, git_access_token=DefaultSecrets.github_token)
+    sb_client = CodebaseClient(repo_config=repo_config, port=get_free_port)
     sb_client.runner = Mock()
     yield sb_client
diff --git a/tests/integration/codemod/test_parse.py b/tests/integration/codemod/test_parse.py
index 9554cf555..06ec7125f 100644
--- a/tests/integration/codemod/test_parse.py
+++ b/tests/integration/codemod/test_parse.py
@@ -5,7 +5,7 @@
 import psutil
 import pytest
 
-from codegen.configs.models.codebase import DefaultCodebaseConfig
+from codegen.configs.models.codebase import CodebaseConfig
 from codegen.git.repo_operator.repo_operator import RepoOperator
 from codegen.sdk.codebase.config import ProjectConfig
 from codegen.sdk.codebase.validation import PostInitValidationStatus, post_init_validation
@@ -26,7 +26,7 @@ def test_codemods_parse(repo: Repo, op: RepoOperator, request) -> None:
     if repo.config is not None:
         codebase_config = repo.config
     else:
-        codebase_config = DefaultCodebaseConfig
+        codebase_config = CodebaseConfig()
 
     codebase_config = codebase_config.model_copy(update={"verify_graph": sync, "debug": log_parse, "ignore_process_errors": False})
 
diff --git a/tests/unit/codegen/runner/sandbox/conftest.py b/tests/unit/codegen/runner/sandbox/conftest.py
index 925286ac2..efc4913cf 100644
--- a/tests/unit/codegen/runner/sandbox/conftest.py
+++ b/tests/unit/codegen/runner/sandbox/conftest.py
@@ -31,4 +31,4 @@ def runner(codebase: Codebase, tmpdir):
             mock_init_codebase.return_value = codebase
             mock_op.return_value = codebase.op
 
-            yield SandboxRunner(repo_config=codebase.op.repo_config, access_token="test-token")
+            yield SandboxRunner(repo_config=codebase.op.repo_config)