diff --git a/.vscode/launch.json b/.vscode/launch.json
index 151b757da..5a052a112 100644
--- a/.vscode/launch.json
+++ b/.vscode/launch.json
@@ -6,9 +6,9 @@
       "type": "pickString",
       "description": "Select the process to debug",
       "options": [
-        "selfdrive/controls/controlsd.py",
-        "system/timed/timed.py",
-        "tools/sim/run_bridge.py"
+        "openpilot/selfdrive/controls/controlsd.py",
+        "openpilot/system/timed/timed.py",
+        "openpilot/tools/sim/run_bridge.py"
       ]
     },
     {
@@ -16,7 +16,7 @@
       "type": "pickString",
       "description": "Select the process to debug",
       "options": [
-        "selfdrive/ui/ui"
+        "openpilot/selfdrive/ui/ui"
       ]
     },
     {
diff --git a/.vscode/settings.json b/.vscode/settings.json
index 811306f39..68f6b9037 100644
--- a/.vscode/settings.json
+++ b/.vscode/settings.json
@@ -17,10 +17,5 @@
     "**/.git",
     "**/.venv",
     "**/__pycache__",
-    // exclude directories that should be using the symlinked version
-    "common/**",
-    "selfdrive/**",
-    "system/**",
-    "tools/**",
   ]
 }
diff --git a/docs/concepts/logs.md b/docs/concepts/logs.md
index 8ba2486ab..dd954d4c7 100644
--- a/docs/concepts/logs.md
+++ b/docs/concepts/logs.md
@@ -2,7 +2,7 @@
 
 openpilot records routes in one minute chunks called segments. A route starts on the rising edge of ignition and ends on the falling edge.
 
-Check out our [Python library](https://github.com/commaai/openpilot/blob/master/openpilot/tools/lib/logreader.py) for reading openpilot logs. Also checkout our [tools](https://github.com/commaai/openpilot/tree/master/tools) to replay and view your data. These are the same tools we use to debug and develop openpilot.
+Check out our [Python library](https://github.com/commaai/openpilot/blob/master/openpilot/tools/lib/logreader.py) for reading openpilot logs. Also checkout our [tools](https://github.com/commaai/openpilot/tree/master/openpilot/tools) to replay and view your data. These are the same tools we use to debug and develop openpilot.
 
 For each segment, openpilot records the following log types:
 
diff --git a/openpilot/tools/CTF.md b/openpilot/tools/CTF.md
index b8acc46fe..2b877a0e2 100644
--- a/openpilot/tools/CTF.md
+++ b/openpilot/tools/CTF.md
@@ -5,7 +5,7 @@ Welcome to the first part of the comma CTF!
 * there's 2 flags in each segment, with roughly increasing difficulty
 * everything you'll need to find the flags is in the openpilot repo
   * grep is also your friend
-  * first, [setup](https://github.com/commaai/openpilot/tree/master/tools#setup-your-pc) your PC
+  * first, [setup](https://github.com/commaai/openpilot/tree/master/openpilot/tools#setup-your-pc) your PC
   * read the docs & checkout out the tools in openpilot/tools/
   * tip: once you get the replay and UI up, start by familiarizing yourself with seeking in replay
 
diff --git a/openpilot/tools/jotpluggler/app.cc b/openpilot/tools/jotpluggler/app.cc
index f80443e56..01eec1536 100644
--- a/openpilot/tools/jotpluggler/app.cc
+++ b/openpilot/tools/jotpluggler/app.cc
@@ -49,7 +49,7 @@ std::string layout_name_from_arg(const std::string &layout_arg) {
 }
 
 fs::path layouts_dir() {
-  return repo_root() / "tools" / "jotpluggler" / "layouts";
+  return repo_root() / "openpilot" / "tools" / "jotpluggler" / "layouts";
 }
 
 std::string sanitize_layout_stem(std::string_view name) {
@@ -249,7 +249,7 @@ void configure_style() {
   g_ui_font = nullptr;
   g_ui_bold_font = nullptr;
   g_mono_font = nullptr;
-  const fs::path fonts_dir = repo_root() / "selfdrive" / "assets" / "fonts";
+  const fs::path fonts_dir = repo_root() / "openpilot" / "selfdrive" / "assets" / "fonts";
   ImFontConfig font_cfg;
   font_cfg.OversampleH = 2;
   font_cfg.OversampleV = 2;
diff --git a/openpilot/tools/jotpluggler/custom_series.cc b/openpilot/tools/jotpluggler/custom_series.cc
index aabf78a0d..70b3e8c3c 100644
--- a/openpilot/tools/jotpluggler/custom_series.cc
+++ b/openpilot/tools/jotpluggler/custom_series.cc
@@ -189,7 +189,7 @@ PythonEvalResult evaluate_custom_python_series(const AppSession &session,
 
     const CommandResult process = run_process_capture_output({
       "python3",
-      (repo_root() / "tools" / "jotpluggler" / "math_eval.py").string(),
+      (repo_root() / "openpilot" / "tools" / "jotpluggler" / "math_eval.py").string(),
       manifest_path.string(),
       globals_path.string(),
       code_path.string(),
diff --git a/openpilot/tools/jotpluggler/layout.cc b/openpilot/tools/jotpluggler/layout.cc
index bf2a3f208..dc7109808 100644
--- a/openpilot/tools/jotpluggler/layout.cc
+++ b/openpilot/tools/jotpluggler/layout.cc
@@ -274,7 +274,7 @@ std::string default_dbc_template() {
 }
 
 DbcEditorSource resolve_dbc_editor_source(const std::string &dbc_name) {
-  const fs::path generated_dbc_dir = repo_root() / "tools" / "jotpluggler" / "generated_dbcs";
+  const fs::path generated_dbc_dir = repo_root() / "openpilot" / "tools" / "jotpluggler" / "generated_dbcs";
   const std::array<DbcEditorSource, 2> candidates = {{
     {.path = repo_root() / "opendbc" / "dbc" / (dbc_name + ".dbc"), .kind = DbcEditorState::SourceKind::Opendbc},
     {.path = generated_dbc_dir / (dbc_name + ".dbc"), .kind = DbcEditorState::SourceKind::Generated},
@@ -334,7 +334,7 @@ bool save_dbc_editor_contents(AppSession *session, UiState *state) {
   }
   try {
     dbc::Database::fromContent(editor.text, editor.save_name + ".dbc");
-    const fs::path generated_dbc_dir = repo_root() / "tools" / "jotpluggler" / "generated_dbcs";
+    const fs::path generated_dbc_dir = repo_root() / "openpilot" / "tools" / "jotpluggler" / "generated_dbcs";
     fs::create_directories(generated_dbc_dir);
     const fs::path output = generated_dbc_dir / (editor.save_name + ".dbc");
     write_file_or_throw(output, editor.text);
diff --git a/openpilot/tools/jotpluggler/sketch_layout.cc b/openpilot/tools/jotpluggler/sketch_layout.cc
index 143a6f5a1..fcc4b183d 100644
--- a/openpilot/tools/jotpluggler/sketch_layout.cc
+++ b/openpilot/tools/jotpluggler/sketch_layout.cc
@@ -386,7 +386,7 @@ std::vector<std::string> available_dbc_names_impl() {
   std::set<std::string> names;
   for (const fs::path &dbc_dir : {
          repo_root() / "opendbc" / "dbc",
-         repo_root() / "tools" / "jotpluggler" / "generated_dbcs",
+         repo_root() / "openpilot" / "tools" / "jotpluggler" / "generated_dbcs",
        }) {
     if (fs::exists(dbc_dir) && fs::is_directory(dbc_dir)) {
       for (const auto &entry : fs::directory_iterator(dbc_dir)) {
@@ -408,7 +408,7 @@ std::vector<std::string> available_dbc_names_impl() {
 fs::path resolve_dbc_path(const std::string &dbc_name) {
   for (const fs::path &candidate : {
          repo_root() / "opendbc" / "dbc" / (dbc_name + ".dbc"),
-         repo_root() / "tools" / "jotpluggler" / "generated_dbcs" / (dbc_name + ".dbc"),
+         repo_root() / "openpilot" / "tools" / "jotpluggler" / "generated_dbcs" / (dbc_name + ".dbc"),
        }) {
     if (fs::exists(candidate)) return candidate;
   }
diff --git a/pyproject.toml b/pyproject.toml
index b844145a4..54f67d629 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -182,10 +182,6 @@ exclude = [
 lint.flake8-implicit-str-concat.allow-multiline = false
 
 [tool.ruff.lint.flake8-tidy-imports.banned-api]
-"selfdrive".msg = "Use openpilot.selfdrive"
-"common".msg = "Use openpilot.common"
-"system".msg = "Use openpilot.system"
-"tools".msg = "Use openpilot.tools"
 "pytest.main".msg = "pytest.main requires special handling that is easy to mess up!"
 "unittest".msg = "Use pytest"
 "time.time".msg = "Use time.monotonic"