fix: remove secrets prefix

.github/workflows/unit-tests.yml

@@ -141,7 +141,7 @@ jobs:
         timeout-minutes: 5
         env:
           GITHUB_WORKSPACE: $GITHUB_WORKSPACE
-          SECRETS_GITHUB_TOKEN: ${{ secrets.GHA_PAT }}
+          GITHUB_TOKEN: ${{ secrets.GHA_PAT }}
         run: |
           uv run pytest \
             -n auto \

src/codegen/cli/auth/session.py

@@ -30,7 +30,7 @@
         self.repo_path = repo_path
         self.local_git = LocalGitRepo(repo_path=repo_path)
         self.codegen_dir = repo_path / CODEGEN_DIR_NAME
-        self.config = UserConfig(env_filepath=self.codegen_dir / ENV_FILENAME)
+        self.config = UserConfig(env_filepath=repo_path / ENV_FILENAME)
         self.config.secrets.github_token = git_token or self.config.secrets.github_token
         self.existing = session_manager.get_session(repo_path) is not None
 
@@ -77,11 +77,11 @@
 
         try:
             if git_token is not None:
                 Github(login_or_token=git_token).get_repo(self.local_git.full_name)
         except BadCredentialsException:
             rich.print(format_command(f"\n[bold red]Error:[/bold red] Invalid GitHub token={git_token} for repo={self.local_git.full_name}"))
             rich.print("[white]Please provide a valid GitHub token for this repository.[/white]")
             raise click.Abort()
 
     def __str__(self) -> str:
         return f"CodegenSession(user={self.config.repository.user_name}, repo={self.config.repository.repo_name})"

src/codegen/cli/commands/config/main.py

@@ -1,11 +1,10 @@
 import logging
-from itertools import groupby
 
 import rich
 import rich_click as click
 from rich.table import Table
 
-from codegen.shared.configs.constants import CODEGEN_DIR_NAME, ENV_FILENAME, GLOBAL_ENV_FILE
+from codegen.shared.configs.constants import ENV_FILENAME, GLOBAL_ENV_FILE
 from codegen.shared.configs.session_manager import session_manager
 from codegen.shared.configs.user_config import UserConfig
 
@@ -43,14 +42,39 @@ def flatten_dict(data: dict, prefix: str = "") -> dict:
     table.add_column("Key", style="cyan", no_wrap=True)
     table.add_column("Value", style="magenta")
 
-    # Group by prefix (before underscore)
-    def get_prefix(item):
-        return item[0].split("_")[0]
+    # Group items by prefix
+    codebase_items = []
+    repository_items = []
+    other_items = []
+
+    for key, value in sorted_items:
+        prefix = key.split("_")[0].lower()
+        if prefix == "codebase":
+            codebase_items.append((key, value))
+        elif prefix == "repository":
+            repository_items.append((key, value))
+        else:
+            other_items.append((key, value))
+
+    # Add codebase section
+    if codebase_items:
+        table.add_section()
+        table.add_row("[bold yellow]Codebase[/bold yellow]", "")
+        for key, value in codebase_items:
+            table.add_row(f"  {key}", str(value))
+
+    # Add repository section
+    if repository_items:
+        table.add_section()
+        table.add_row("[bold yellow]Repository[/bold yellow]", "")
+        for key, value in repository_items:
+            table.add_row(f"  {key}", str(value))
 
-    for prefix, group in groupby(sorted_items, key=get_prefix):
+    # Add other section
+    if other_items:
         table.add_section()
-        table.add_row(f"[bold yellow]{prefix.title()}[/bold yellow]", "")
-        for key, value in group:
+        table.add_row("[bold yellow]Other[/bold yellow]", "")
+        for key, value in other_items:
             table.add_row(f"  {key}", str(value))
 
     rich.print(table)
@@ -91,13 +115,13 @@ def set_command(key: str, value: str, is_global: bool):
             rich.print(f"[red]{e}[/red]")
             return
 
-    rich.print(f"[green]Successfully set {key}=[magenta]{value}[/magenta] and saved to .env[/green]")
+    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:
         env_filepath = GLOBAL_ENV_FILE
     else:
-        env_filepath = active_session_path / CODEGEN_DIR_NAME / ENV_FILENAME
+        env_filepath = active_session_path / ENV_FILENAME
 
     return UserConfig(env_filepath)

src/codegen/cli/commands/init/render.py

@@ -4,7 +4,6 @@
 def get_success_message(codegen_dir: Path, docs_dir: Path, examples_dir: Path) -> str:
     """Get the success message to display after initialization."""
     return """📁 .codegen configuration folder created:
-   [dim].env[/dim]                       Project configuration
    [dim]codemods/[/dim]                  Your codemod implementations
    [dim].venv/[/dim]                     Python virtual environment (gitignored)
    [dim]codegen-system-prompt.txt[/dim]  AI system prompt (gitignored)"""

src/codegen/cli/mcp/resources/system_prompt.py

@@ -524,7 +524,6 @@ def baz():
    ```bash
    .codegen/
    ├── .venv/            # Python virtual environment (gitignored)
-   ├── .env              # Project configuration
    ├── codemods/         # Your codemod implementations
    ├── jupyter/          # Jupyter notebooks for exploration
    └── codegen-system-prompt.txt  # AI system prompt

src/codegen/cli/workspace/initialize_workspace.py

@@ -50,7 +50,7 @@
         CODEMODS_DIR.mkdir(parents=True, exist_ok=True)
 
         # Initialize virtual environment
         status_obj.update(f"   {'Creating' if isinstance(status, str) else 'Checking'} virtual environment...")
         venv = VenvManager(session.codegen_dir)
         if not venv.is_initialized():
             venv.create_venv()
@@ -64,7 +64,7 @@
         except Exception as e:
             rich.print(f"[yellow]Warning: Could not download system prompt: {e}[/yellow]")
 
         status_obj.update(f"   {'Updating' if isinstance(status, Status) else status} .gitignore...")
         modify_gitignore(CODEGEN_FOLDER)
 
         # Create notebook template
@@ -72,14 +72,14 @@
 
         # Only fetch docs and examples if requested and session is provided
         if fetch_docs and session:
             status_obj.update("Fetching latest docs & examples...")
             shutil.rmtree(DOCS_FOLDER, ignore_errors=True)
             shutil.rmtree(EXAMPLES_FOLDER, ignore_errors=True)
 
             DOCS_FOLDER.mkdir(parents=True, exist_ok=True)
             EXAMPLES_FOLDER.mkdir(parents=True, exist_ok=True)
 
             response = RestAPI(get_current_token()).get_docs()
             populate_api_docs(DOCS_FOLDER, response.docs, status_obj)
             populate_examples(session, EXAMPLES_FOLDER, response.examples, status_obj)
 
@@ -105,7 +105,6 @@
         "prompts/",
         "jupyter/",
         ".venv/",  # Add venv to gitignore
-        ".env",
         "codegen-system-prompt.txt",
         "",
         "# Python cache files",

src/codegen/shared/configs/models/base_config.py

@@ -5,7 +5,7 @@
 from pydantic_settings import BaseSettings, SettingsConfigDict
 
 from codegen.shared.configs.constants import ENV_FILENAME, GLOBAL_ENV_FILE
-from codegen.shared.configs.session_manager import session_codegen_dir
+from codegen.shared.configs.session_manager import session_root
 
 
 class BaseConfig(BaseSettings, ABC):
@@ -18,9 +18,9 @@ class BaseConfig(BaseSettings, ABC):
 
     def __init__(self, prefix: str, env_filepath: Path | None = None, *args, **kwargs) -> None:
         if env_filepath is None:
-            codegen_dir = session_codegen_dir
-            if codegen_dir is not None:
-                env_filepath = codegen_dir / ENV_FILENAME
+            root_path = session_root
+            if root_path is not None:
+                env_filepath = root_path / ENV_FILENAME
 
         # Only include env files that exist
         env_filepaths = []
@@ -29,7 +29,7 @@ def __init__(self, prefix: str, env_filepath: Path | None = None, *args, **kwarg
         if env_filepath and env_filepath.exists() and env_filepath != GLOBAL_ENV_FILE:
             env_filepaths.append(env_filepath)
 
-        self.model_config["env_prefix"] = f"{prefix.upper()}_"
+        self.model_config["env_prefix"] = f"{prefix.upper()}_" if len(prefix) > 0 else ""
         self.model_config["env_file"] = env_filepaths
 
         super().__init__(*args, **kwargs)

src/codegen/shared/configs/models/secrets.py

@@ -8,11 +8,12 @@
     Falls back to .env file for missing values.
     """
 
-    def __init__(self, prefix: str = "SECRETS", *args, **kwargs) -> None:
+    def __init__(self, prefix: str = "", *args, **kwargs) -> None:
         super().__init__(prefix=prefix, *args, **kwargs)
 
     github_token: str | None = None
     openai_api_key: str | None = None
+    linear_api_key: str | None = None
 
 
 DefaultSecrets = SecretsConfig()

src/codegen/shared/configs/session_manager.py

@@ -48,7 +48,7 @@
         with open(SESSION_FILE, "w") as f:
             json.dump(self.__dict__(), f)
 
     def __dict__(self) -> dict:
         return {
             "active_session_path": self.active_session_path,
             "sessions": self.sessions,
@@ -58,14 +58,14 @@
         active = self.active_session_path or "None"
         sessions_str = "\n    ".join(self.sessions) if self.sessions else "None"
 
         return f"GlobalConfig:\n  Active Session: {active}\n  Sessions:\n    {sessions_str}\n  Global Session:\n    {self.session_config}"
 
 
-def _get_codegen_dir() -> Path | None:
+def _get_project_root() -> Path | None:
     """Get the active codegen directory."""
     active_session = session_manager.get_active_session()
     if active_session:
-        return active_session / CODEGEN_DIR_NAME
+        return active_session
 
     try:
         path = Path.cwd().resolve()
@@ -78,9 +78,9 @@
         git_path = path / ".git"
 
         if codegen_path.exists():
-            return codegen_path
+            return path
         if git_path.exists():
-            return codegen_path
+            return path
 
         parent = path.parent.resolve()
         if parent == path:  # We've reached the root directory
@@ -91,4 +91,4 @@
 
 
 session_manager = SessionManager()
-session_codegen_dir = _get_codegen_dir()
+session_root = _get_project_root()

src/codegen/shared/configs/user_config.py

@@ -59,10 +59,10 @@ def set(self, full_key: str, value: str) -> None:
         match f"{prefix}_":
             case self.repository.env_prefix:
                 self.repository.set(self.env_filepath, key, value)
-            case self.secrets.env_prefix:
-                self.secrets.set(self.env_filepath, key, value)
             case self.codebase.env_prefix:
                 self.codebase.set(self.env_filepath, key, value)
+            case _:
+                self.secrets.set(self.env_filepath, full_key, value)
 
     def __str__(self) -> str:
         """Return a pretty-printed string representation of the config."""