diff --git a/.codegen/.gitignore b/.codegen/.gitignore
index a384b9257..77d89d205 100644
--- a/.codegen/.gitignore
+++ b/.codegen/.gitignore
@@ -8,12 +8,8 @@ jupyter/
 codegen-system-prompt.txt
 
 # Python cache files
-__pycache__/
+**/__pycache__/
 *.py[cod]
 *$py.class
 *.txt
 *.pyc
-
-# Keep codemods
-!codemods/
-!codemods/**
diff --git a/.codegen/codemods/no_link_backticks/no_link_backticks.py b/.codegen/codemods/no_link_backticks/no_link_backticks.py
index b74509cc6..e8cda5323 100644
--- a/.codegen/codemods/no_link_backticks/no_link_backticks.py
+++ b/.codegen/codemods/no_link_backticks/no_link_backticks.py
@@ -2,7 +2,7 @@
 from codegen import Codebase
 
 
-@codegen.function("no-link-backticks")
+@codegen.function(name="no-link-backticks", subdirectories=["test/unit"])
 def run(codebase: Codebase):
     import re
 
@@ -12,6 +12,7 @@ def run(codebase: Codebase):
     # Iterate over all .mdx files in the codebase
     for file in codebase.files(extensions=["mdx"]):
         if file.extension == ".mdx":
+            print(f"Processing {file.path}")
             new_content = file.content
 
             # Find all markdown links with backticks in link text
diff --git a/src/codegen/cli/commands/list/main.py b/src/codegen/cli/commands/list/main.py
index 046c1a17e..944828e3c 100644
--- a/src/codegen/cli/commands/list/main.py
+++ b/src/codegen/cli/commands/list/main.py
@@ -17,10 +17,16 @@ def list_command():
         table.add_column("Name", style="cyan")
         table.add_column("Type", style="magenta")
         table.add_column("Path", style="dim")
+        table.add_column("Subdirectories", style="dim")
 
         for func in functions:
             func_type = "Webhook" if func.lint_mode else "Function"
-            table.add_row(func.name, func_type, str(func.filepath.relative_to(Path.cwd())) if func.filepath else "<unknown>")
+            table.add_row(
+                func.name,
+                func_type,
+                str(func.filepath.relative_to(Path.cwd())) if func.filepath else "<unknown>",
+                ", ".join(func.subdirectories) if func.subdirectories else "",
+            )
 
         rich.print(table)
         rich.print("\nRun a function with:")
diff --git a/src/codegen/cli/commands/run/main.py b/src/codegen/cli/commands/run/main.py
index 1c393abfe..d34d93784 100644
--- a/src/codegen/cli/commands/run/main.py
+++ b/src/codegen/cli/commands/run/main.py
@@ -13,14 +13,12 @@
 @click.command(name="run")
 @requires_init
 @click.argument("label", required=True)
-@click.option("--path", type=str, help="Path to build the codebase from. Defaults to the repo root.")
 @click.option("--web", is_flag=True, help="Run the function on the web service instead of locally")
 @click.option("--diff-preview", type=int, help="Show a preview of the first N lines of the diff")
 @click.option("--arguments", type=str, help="Arguments as a json string to pass as the function's 'arguments' parameter")
 def run_command(
     session: CodegenSession,
     label: str,
-    path: str | None = None,
     web: bool = False,
     diff_preview: int | None = None,
     arguments: str | None = None,
@@ -59,4 +57,4 @@ def run_command(
     else:
         from codegen.cli.commands.run.run_local import run_local
 
-        run_local(session, codemod, diff_preview=diff_preview, path=path)
+        run_local(session, codemod, diff_preview=diff_preview)
diff --git a/src/codegen/cli/commands/run/run_local.py b/src/codegen/cli/commands/run/run_local.py
index 4f030b4fa..8e2afdfea 100644
--- a/src/codegen/cli/commands/run/run_local.py
+++ b/src/codegen/cli/commands/run/run_local.py
@@ -6,10 +6,16 @@
 
 from codegen.cli.auth.session import CodegenSession
 from codegen.cli.utils.function_finder import DecoratedFunction
+from codegen.git.repo_operator.repo_operator import RepoOperator
+from codegen.git.schemas.repo_config import RepoConfig
+from codegen.sdk.codebase.config import ProjectConfig
 from codegen.sdk.core.codebase import Codebase
 
 
-def parse_codebase(repo_root: Path) -> Codebase:
+def parse_codebase(
+    repo_path: Path,
+    subdirectories: list[str] | None = None,
+) -> Codebase:
     """Parse the codebase at the given root.
 
     Args:
@@ -18,7 +24,14 @@ def parse_codebase(repo_root: Path) -> Codebase:
     Returns:
         Parsed Codebase object
     """
-    codebase = Codebase(repo_root)
+    codebase = Codebase(
+        projects=[
+            ProjectConfig(
+                repo_operator=RepoOperator(repo_config=RepoConfig.from_repo_path(repo_path=repo_path)),
+                subdirectories=subdirectories,
+            )
+        ]
+    )
     return codebase
 
 
@@ -26,7 +39,6 @@ def run_local(
     session: CodegenSession,
     function: DecoratedFunction,
     diff_preview: int | None = None,
-    path: Path | None = None,
 ) -> None:
     """Run a function locally against the codebase.
 
@@ -36,10 +48,8 @@ def run_local(
         diff_preview: Number of lines of diff to preview (None for all)
     """
     # Parse codebase and run
-    codebase_path = f"{session.repo_path}/{path}" if path else session.repo_path
-
-    with Status(f"[bold]Parsing codebase at {codebase_path} ...", spinner="dots") as status:
-        codebase = parse_codebase(codebase_path)
+    with Status(f"[bold]Parsing codebase at {session.repo_path} with subdirectories {function.subdirectories or 'ALL'} ...", spinner="dots") as status:
+        codebase = parse_codebase(repo_path=session.repo_path, subdirectories=function.subdirectories)
         status.update("[bold green]✓ Parsed codebase")
 
         status.update("[bold]Running codemod...")
diff --git a/src/codegen/cli/sdk/decorator.py b/src/codegen/cli/sdk/decorator.py
index e4e93e956..3a9d7938b 100644
--- a/src/codegen/cli/sdk/decorator.py
+++ b/src/codegen/cli/sdk/decorator.py
@@ -15,11 +15,13 @@ def __init__(
         self,
         name: str,
         *,
+        subdirectories: list[str] | None = None,
         webhook_config: dict | None = None,
         lint_mode: bool = False,
         lint_user_whitelist: Sequence[str] | None = None,
     ):
         self.name = name
+        self.subdirectories = subdirectories
         self.func: Callable | None = None
         self.params_type = None
         self.webhook_config = webhook_config
@@ -42,7 +44,7 @@ def wrapper(*args: P.args, **kwargs: P.kwargs) -> T:
         return wrapper
 
 
-def function(name: str) -> DecoratedFunction:
+def function(name: str, subdirectories: list[str] | None = None) -> DecoratedFunction:
     """Decorator for codegen functions.
 
     Args:
@@ -54,7 +56,7 @@ def run(codebase):
             pass
 
     """
-    return DecoratedFunction(name)
+    return DecoratedFunction(name=name, subdirectories=subdirectories)
 
 
 def webhook(
diff --git a/src/codegen/cli/utils/function_finder.py b/src/codegen/cli/utils/function_finder.py
index 0d77a71fd..325dece3f 100644
--- a/src/codegen/cli/utils/function_finder.py
+++ b/src/codegen/cli/utils/function_finder.py
@@ -14,6 +14,7 @@ class DecoratedFunction:
     source: str
     lint_mode: bool
     lint_user_whitelist: list[str]
+    subdirectories: list[str] | None = None
     filepath: Path | None = None
     parameters: list[tuple[str, str | None]] = dataclasses.field(default_factory=list)
     arguments_type_schema: dict | None = None
@@ -83,6 +84,20 @@ class CodegenFunctionVisitor(ast.NodeVisitor):
     def __init__(self):
         self.functions: list[DecoratedFunction] = []
 
+    def get_function_name(self, node: ast.Call) -> str:
+        keywords = {k.arg: k.value for k in node.keywords}
+        if "name" in keywords:
+            return ast.literal_eval(keywords["name"])
+        return ast.literal_eval(node.args[0])
+
+    def get_subdirectories(self, node: ast.Call) -> list[str] | None:
+        keywords = {k.arg: k.value for k in node.keywords}
+        if "subdirectories" in keywords:
+            return ast.literal_eval(keywords["subdirectories"])
+        if len(node.args) > 1:
+            return ast.literal_eval(node.args[1])
+        return None
+
     def get_function_body(self, node: ast.FunctionDef) -> str:
         """Extract and unindent the function body."""
         # Get the start and end positions of the function body
@@ -178,7 +193,7 @@ def visit_FunctionDef(self, node):
         for decorator in node.decorator_list:
             if (
                 isinstance(decorator, ast.Call)
-                and len(decorator.args) >= 1
+                and (len(decorator.args) > 0 or len(decorator.keywords) > 0)
                 and (
                     # Check if it's a direct codegen.X call
                     (isinstance(decorator.func, ast.Attribute) and isinstance(decorator.func.value, ast.Name) and decorator.func.value.id == "codegen")
@@ -188,7 +203,8 @@ def visit_FunctionDef(self, node):
                 )
             ):
                 # Get the function name from the decorator argument
-                func_name = ast.literal_eval(decorator.args[0])
+                func_name = self.get_function_name(decorator)
+                subdirectories = self.get_subdirectories(decorator)
 
                 # Get additional metadata for webhook
                 lint_mode = decorator.func.attr == "webhook"
@@ -201,7 +217,16 @@ def visit_FunctionDef(self, node):
                 # Get just the function body, unindented
                 body_source = self.get_function_body(node)
                 parameters = self.get_function_parameters(node)
-                self.functions.append(DecoratedFunction(name=func_name, source=body_source, lint_mode=lint_mode, lint_user_whitelist=lint_user_whitelist, parameters=parameters))
+                self.functions.append(
+                    DecoratedFunction(
+                        name=func_name,
+                        subdirectories=subdirectories,
+                        source=body_source,
+                        lint_mode=lint_mode,
+                        lint_user_whitelist=lint_user_whitelist,
+                        parameters=parameters,
+                    )
+                )
 
     def _has_codegen_root(self, node):
         """Recursively check if an AST node chain starts with codegen."""