diff --git a/.circleci/ats.sh b/.circleci/ats.sh
index 8d0bcb3cf..0177e8494 100755
--- a/.circleci/ats.sh
+++ b/.circleci/ats.sh
@@ -33,4 +33,3 @@ if [ ! -s codecov_ats/tests_to_run.txt ]; then
     run_count=1
     echo "Added ${TESTS_TO_RUN} as fallback. New run count: $run_count"
 fi
-
diff --git a/.circleci/config.yml b/.circleci/config.yml
index ab288240d..46d2b5cd8 100644
--- a/.circleci/config.yml
+++ b/.circleci/config.yml
@@ -528,6 +528,3 @@ workflows:
           requires:
             - linux-wheels
             - osx-wheels
-
-
-
diff --git a/.github/codecov.yml b/.github/codecov.yml
index c943f5891..defec98ab 100644
--- a/.github/codecov.yml
+++ b/.github/codecov.yml
@@ -71,4 +71,3 @@ cli:
         - "--verbose"
         - "-n=auto"
       python_path: ".venv/bin/python"
-
diff --git a/.gitignore b/.gitignore
index 4b1da69de..ef6b42612 100644
--- a/.gitignore
+++ b/.gitignore
@@ -65,4 +65,4 @@ graph-sitter-types/typings/**
 coverage.json
 tests/integration/verified_codemods/codemod_data/repo_commits.json
 .codegen/*
-.benchmarks/*
\ No newline at end of file
+.benchmarks/*
diff --git a/.lfsconfig b/.lfsconfig
index ce560ac64..f1ff0bb49 100644
--- a/.lfsconfig
+++ b/.lfsconfig
@@ -1,2 +1,2 @@
 [lfs]
-	url = git@github.com:codegen-sh/graph-sitter-private.git
\ No newline at end of file
+	url = git@github.com:codegen-sh/graph-sitter-private.git
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index e147af2bc..a1c6f407b 100644
--- a/.pre-commit-config.yaml
+++ b/.pre-commit-config.yaml
@@ -43,7 +43,7 @@ repos:
         exclude_types: [mdx, pyi]
       - id: check-yaml
       - id: end-of-file-fixer
-        files: .*/expected_diff.patch
+        exclude: (src/codemods/eval)|(tests/unit/skills/snapshots)|(tests/unit/codegen/sdk/output)|(tests/integration/verified_codemods)|(docs/)
       - id: check-merge-conflict
 
   - repo: https://github.com/python-jsonschema/check-jsonschema
@@ -80,6 +80,13 @@ repos:
         entry: scripts/disallowed-words-check.sh
         language: script
         files: ''  # Check all files
+      - id: generate-runner-imports
+        name: Generate Runner Imports
+        entry: bash -c "uv run --frozen python -m codegen.gscli.main generate runner-imports src/codegen/shared/compilation/function_imports.py"
+        language: system
+        pass_filenames: false
+        always_run: true
+
   - repo: https://github.com/renovatebot/pre-commit-hooks
     rev: 39.120.4
     hooks:
diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md
index 3d27630db..1be7c5304 100644
--- a/CONTRIBUTING.md
+++ b/CONTRIBUTING.md
@@ -69,4 +69,3 @@ git push origin v0.YOUR_VERSION
 ```
 
 This will trigger a release job to build this new version.
-
diff --git a/mypy.ini b/mypy.ini
index 5d62d120b..d186be42f 100644
--- a/mypy.ini
+++ b/mypy.ini
@@ -49,4 +49,3 @@ exclude = (?x)(
           | tests/unit/skills/snapshots/*
     )
 plugins = pydantic.mypy
-
diff --git a/pyproject.toml b/pyproject.toml
index 48fc6d5e0..b633effaf 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -153,14 +153,7 @@ max-line-length = 200
 
 [tool.ruff]
 line-length = 200
-exclude = [
-  "app/codemod/compilation/function_imports.py", # generated import list to compile uesr code with
-  'codegen_tests/**/expected*/**',
-  'codegen_tests/**/original/**',
-  'codegen_tests/projects/**/codebase/**',
-  'docs/**',
-  'scripts/Debugging/**',
-]
+exclude = ["src/codegen/shared/compilation/function_imports.py", 'docs/**']
 
 lint.select = ["F", "E", "W", "I", "UP", "D", "RUF", "DTZ"]
 lint.ignore = [
@@ -192,9 +185,8 @@ lint.exclude = [
 ] # disable just linting for notebooks (allow for formatting)
 lint.pydocstyle.convention = "google"
 [tool.ruff.lint.isort]
-known-first-party = ["app"]
-known-third-party = ["git"]
-#known-local-folder=[]
+known-first-party = ["codegen"]
+
 [tool.coverage.run]
 branch = true
 plugins = ["Cython.Coverage"]
diff --git a/scripts/setup-lfs.sh b/scripts/setup-lfs.sh
index e69ad1e4e..5325aacae 100755
--- a/scripts/setup-lfs.sh
+++ b/scripts/setup-lfs.sh
@@ -2,4 +2,4 @@
 ./scripts/install-deps.sh
 
 git lfs install
-git lfs pull
\ No newline at end of file
+git lfs pull
diff --git a/scripts/setup.sh b/scripts/setup.sh
index 2e98a41c1..0a120eac2 100755
--- a/scripts/setup.sh
+++ b/scripts/setup.sh
@@ -6,4 +6,4 @@ uv tool update-shell
 uv venv && source .venv/bin/activate
 uv sync
 pre-commit install
-pre-commit install-hooks
\ No newline at end of file
+pre-commit install-hooks
diff --git a/src/codegen/gsbuild/build.py b/src/codegen/gsbuild/build.py
index 789d23ef1..55b695ffc 100644
--- a/src/codegen/gsbuild/build.py
+++ b/src/codegen/gsbuild/build.py
@@ -21,5 +21,4 @@ class SpecialBuildHook(BuildHookInterface):
     def initialize(self, version: str, build_data: dict[str, Any]) -> None:
         file = Path(self.root) / "src" / "codegen" / "sdk" / "__init__.py"
         update_init_file(file)
-
         build_data["artifacts"].append(f"/{file}")
diff --git a/src/codegen/gscli/__init__.py b/src/codegen/gscli/__init__.py
index 8b1378917..e69de29bb 100644
--- a/src/codegen/gscli/__init__.py
+++ b/src/codegen/gscli/__init__.py
@@ -1 +0,0 @@
-
diff --git a/src/codegen/gscli/generate/commands.py b/src/codegen/gscli/generate/commands.py
index cdc24944a..47c87f79d 100644
--- a/src/codegen/gscli/generate/commands.py
+++ b/src/codegen/gscli/generate/commands.py
@@ -186,3 +186,7 @@ def generate_codegen_sdk_docs(docs_dir: str) -> None:
         json.dump(mint_data, mint_file, indent=2)
 
     print(colored("Updated mint.json with new page sets", "green"))
+
+
+if __name__ == "__main__":
+    generate()
diff --git a/src/codegen/gscli/generate/runner_imports.py b/src/codegen/gscli/generate/runner_imports.py
index 53da72531..02daedbba 100644
--- a/src/codegen/gscli/generate/runner_imports.py
+++ b/src/codegen/gscli/generate/runner_imports.py
@@ -14,6 +14,7 @@
 CODEGEN_IMPORTS = """
 from codegen.git.models.codemod_context import CodemodContext
 from codegen.git.models.github_named_user_context import GithubNamedUserContext
+from codegen.git.models.pr_options import PROptions
 from codegen.git.models.pr_part_context import PRPartContext
 from codegen.git.models.pull_request_context import PullRequestContext
 """
@@ -34,13 +35,16 @@
 {gs_public_imports}
 """.strip()
 
-IMPORT_FILE_TEMPLATE = '''
-# This file is auto-generated, do not modify manually. Edit this in codegen-backend/cli/generate/runner_imports.py.
+IMPORT_FILE_TEMPLATE = (
+    '''
+# This file is auto-generated, do not modify manually. Edit this in src/codegen/gscli/generate/runner_imports.py.
 def get_generated_imports():
     return """
 {import_str}
 """
 '''.strip()
+    + "\n"
+)
 
 
 def get_runner_imports(include_codegen=True, include_private_imports: bool = True) -> str:
diff --git a/src/codegen/runner/sandbox/executor.py b/src/codegen/runner/sandbox/executor.py
index afc15bfd0..6304d694e 100644
--- a/src/codegen/runner/sandbox/executor.py
+++ b/src/codegen/runner/sandbox/executor.py
@@ -53,7 +53,7 @@ async def find_flag_groups(self, code_flags: list[CodeFlag], grouping_config: Gr
 
         # =====[ Group the code flags ]=====
         logger.info(f"> Grouping CodeFlags by config: {grouping_config}")
-        grouper = get_grouper_by_group_by(grouping_config.group_by, repo_id=self.codebase.op.repo_config.id)
+        grouper = get_grouper_by_group_by(grouping_config.group_by)
         groups = grouper.create_all_groups(flags=code_flags, repo_operator=self.codebase.op)
         logger.info(f"> Created {len(groups)} groups")
         return groups
diff --git a/src/codegen/sdk/core/global_context.py b/src/codegen/sdk/core/global_context.py
deleted file mode 100644
index 08e430adb..000000000
--- a/src/codegen/sdk/core/global_context.py
+++ /dev/null
@@ -1,20 +0,0 @@
-from dataclasses import dataclass, field
-from typing import TYPE_CHECKING
-
-from codegen.sdk.codebase.config import DefaultConfig, GraphSitterConfig
-from codegen.sdk.codebase.multigraph import MultiGraph
-from codegen.sdk.core.plugins import PLUGINS
-
-if TYPE_CHECKING:
-    from codegen.sdk.core.codebase import Codebase
-    from codegen.sdk.core.function import Function
-
-
-@dataclass
-class GlobalContext[TFunction: Function]:
-    multigraph: MultiGraph[TFunction] = field(default_factory=MultiGraph)
-    config: GraphSitterConfig = DefaultConfig
-
-    def execute_plugins(self, codebase: "Codebase"):
-        for plugin in PLUGINS:
-            plugin.execute(codebase)
diff --git a/src/codegen/shared/compilation/README.md b/src/codegen/shared/compilation/README.md
index 626ceb7ea..d6913e076 100644
--- a/src/codegen/shared/compilation/README.md
+++ b/src/codegen/shared/compilation/README.md
@@ -5,4 +5,3 @@ This includes:
 - Catching and logging any compilation errors
 - Monkey patching built-ins like print
 - etc
-
diff --git a/src/codegen/shared/compilation/function_imports.py b/src/codegen/shared/compilation/function_imports.py
index 5937d906e..67ce6f0b3 100644
--- a/src/codegen/shared/compilation/function_imports.py
+++ b/src/codegen/shared/compilation/function_imports.py
@@ -1,4 +1,4 @@
-# This file is auto-generated, do not modify manually. Edit this in codegen-backend/cli/generate/runner_imports.py.
+# This file is auto-generated, do not modify manually. Edit this in src/codegen/gscli/generate/runner_imports.py.
 def get_generated_imports():
     return """
 # External imports
@@ -12,10 +12,11 @@ def get_generated_imports():
 
 from codegen.git.models.codemod_context import CodemodContext
 from codegen.git.models.github_named_user_context import GithubNamedUserContext
+from codegen.git.models.pr_options import PROptions
 from codegen.git.models.pr_part_context import PRPartContext
 from codegen.git.models.pull_request_context import PullRequestContext
 
-from codegen.sdk.codebase.control_flow import StopCodemodException
+from codegen.shared.exceptions.control_flow import StopCodemodException
 
 # GraphSitter imports (public)
 from codegen.sdk.codebase.flagging.enums import FlagKwargs