From df8f364587dd8bb3a7b750b6edf2042c63172879 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Anders=20Thors=C3=A9n?=
 <10030664+MickOls@users.noreply.github.com>
Date: Wed, 24 Jun 2026 15:08:12 +0200
Subject: [PATCH 1/2] Clean internal refs and fix docs and CI triggers

---
 .github/workflows/ci.yml                   |   4 +
 README.md                                  |   4 +-
 cosmo_required_fixes.patch                 | 533 +++++++++++++++++++++
 cosmo_required_fixes.patch:Zone.Identifier | Bin 0 -> 25 bytes
 docs/getting-started/quickstart.md         |  11 +-
 src/cosmo/converters/openlabel_to_omega.py |   4 +-
 src/cosmo/gui/main_window.py               |   2 +-
 src/cosmo/gui/workers.py                   |   2 +-
 tests/cli_helpers.py                       |   4 +-
 tests/conftest.py                          |   4 +-
 tests/test_calibration_compute_whitebox.py |   8 +-
 tests/test_console_scripts_smoke.py        |   8 +-
 tests/test_convert_app_e2e_not_smoke.py    |   2 +-
 tests/test_convert_no_scripts_fallback.py  |   4 +-
 tests/test_core_calibrate_whitebox.py      |  14 +-
 tests/test_core_convert_whitebox.py        |  12 +-
 tests/test_integration_mcap_convert_app.py |  10 +-
 tests/test_integration_mcap_converter.py   |  10 +-
 tests/test_integration_mcap_gt_count.py    |  14 +-
 tests/test_main_dispatch.py                |   4 +-
 tests/test_openlabel_to_omega_whitebox.py  |   8 +-
 21 files changed, 599 insertions(+), 63 deletions(-)
 create mode 100644 cosmo_required_fixes.patch
 create mode 100644 cosmo_required_fixes.patch:Zone.Identifier

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index 710b6f8..831b249 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -3,6 +3,10 @@ name: CI
 on:
   push:
   pull_request:
+  workflow_dispatch:
+  schedule:
+    # Run optional/heavier integration tests weekly and on demand.
+    - cron: "0 3 * * 1"
 
 jobs:
   test:
diff --git a/README.md b/README.md
index 8300192..91b1d4b 100644
--- a/README.md
+++ b/README.md
@@ -52,8 +52,8 @@ python -m pip install -e . --group dev
 > tools explicitly: `pip install -e . pytest ruff` (adding `betterosi mcap` for
 > MCAP integration tests).
 
-> Tip 1: The **GUI** is launced with `cosmo` or `cosmo gui`.
-> Tip 2: During development with downloaded repro, all `cosmo` commands can be replaced with `python run_cosmo.py ...`, `cosmo.cmd ...` or `cosmo.ps1 ...`. `python run_gui.py` always starts the **GUI**.
+> Tip 1: The **GUI** is launched with `cosmo` or `cosmo gui`.
+> Tip 2: In headless environments, prefer explicit subcommands such as `cosmo convert ...` rather than plain `cosmo`, which may start the GUI.
 
 Convert using [ORBIT](https://github.com/RI-SE/ORBIT) georef as the primary pixel→ground mapping (**Convert** tab in the **GUI**):
 
diff --git a/cosmo_required_fixes.patch b/cosmo_required_fixes.patch
new file mode 100644
index 0000000..d118fa4
--- /dev/null
+++ b/cosmo_required_fixes.patch
@@ -0,0 +1,533 @@
+--- a/.github/workflows/ci.yml
++++ b/.github/workflows/ci.yml
+@@ -3,6 +3,10 @@
+ on:
+   push:
+   pull_request:
++  workflow_dispatch:
++  schedule:
++    # Run optional/heavier integration tests weekly and on demand.
++    - cron: "0 3 * * 1"
+ 
+ jobs:
+   test:
+--- a/README.md
++++ b/README.md
+@@ -52,8 +52,8 @@
+ > tools explicitly: `pip install -e . pytest ruff` (adding `betterosi mcap` for
+ > MCAP integration tests).
+ 
+-> Tip 1: The **GUI** is launced with `cosmo` or `cosmo gui`.
+-> Tip 2: During development with downloaded repro, all `cosmo` commands can be replaced with `python run_cosmo.py ...`, `cosmo.cmd ...` or `cosmo.ps1 ...`. `python run_gui.py` always starts the **GUI**.
++> Tip 1: The **GUI** is launched with `cosmo` or `cosmo gui`.
++> Tip 2: In headless environments, prefer explicit subcommands such as `cosmo convert ...` rather than plain `cosmo`, which may start the GUI.
+ 
+ Convert using [ORBIT](https://github.com/RI-SE/ORBIT) georef as the primary pixel→ground mapping (**Convert** tab in the **GUI**):
+ 
+--- a/docs/getting-started/quickstart.md
++++ b/docs/getting-started/quickstart.md
+@@ -10,17 +10,16 @@
+ cosmo gui
+ ```
+ 
+-Development shortcut (either of):
++Use the installed console script:
+ 
+ ```bash
+-python run_gui.py # Start GUI
+-python run_cosmo.py gui # Same behaviour as cosmo (when installed)
+-cosmo.cmd gui # Same behaviour in Windows cmd termial as cosmo (when installed)
+-cosmo.ps1 gui # Same behaviour in Windows PowerShell termial as cosmo (when installed)
++cosmo gui
++# or simply:
++cosmo
+ ```
+ ---
+ ## CLI
+-> During development `cosmo ...` can be replaced with `python run_cosmo ...`, `cosmo.exe ...` or `cosmo.ps1 ...` without needing to install cosmo, e.g., `python run_cosmo.py convert ...`. To install for development use `uv sync --group dev` or `pip install -e . --group dev`.
++> For development, install the package first (for example `uv sync --group dev` or `pip install -e . --group dev`) and then use the `cosmo ...` console script.
+ ---
+ ### Convert (recommended: ORBIT georef)
+ 
+--- a/src/cosmo/converters/openlabel_to_omega.py
++++ b/src/cosmo/converters/openlabel_to_omega.py
+@@ -721,7 +721,7 @@
+     # ----------------------------
+     # IMPORTANT:
+     # Use betterosi.Writer as a context manager to ensure MCAP footer/summary are finalized properly. [1](https://deepwiki.com/ika-rwth-aachen/omega-prime/3.1-loading-and-saving-recordings)[4](https://ika-rwth-aachen.github.io/omega-prime/notebooks/tutorial/)
+-    # Also write topic names without leading "/" to match common omega-prime usage. [3](https://risecloud-my.sharepoint.com/personal/anders_thorsen_ri_se/Documents/Microsoft%20Copilot%20Chat%20Files/convert_app.py)[2](https://risecloud-my.sharepoint.com/personal/anders_thorsen_ri_se/Documents/Microsoft%20Copilot%20Chat%20Files/openlabel_to_omega.py)
++    # Also write topic names without leading "/" to match common omega-prime usage.
+ 
+     def _write_map(writer_mcap):
+         if odr_path and os.path.isfile(odr_path):
+@@ -752,7 +752,7 @@
+             gt.proj_string = _gt_proj_string
+         if _gt_country_code:
+             gt.country_code = _gt_country_code
+-        # Provide log_time explicitly; readers often build indices from it. [4](https://ika-rwth-aachen.github.io/omega-prime/notebooks/tutorial/)[3](https://risecloud-my.sharepoint.com/personal/anders_thorsen_ri_se/Documents/Microsoft%20Copilot%20Chat%20Files/convert_app.py)
++        # Provide log_time explicitly; readers often build indices from it. [4](https://ika-rwth-aachen.github.io/omega-prime/notebooks/tutorial/)
+         writer_mcap.add(gt, topic="ground_truth", log_time=total_nanos)
+ 
+     # If MCAP enabled, write with context manager; else only build CSV rows
+--- a/src/cosmo/gui/main_window.py
++++ b/src/cosmo/gui/main_window.py
+@@ -9,7 +9,7 @@
+ from pathlib import Path
+ from typing import Optional
+ 
+-# Qt binding selection: PyQt5 → PySide6 → PyQt6 (same as your current GUI). [1](https://risecloud-my.sharepoint.com/personal/anders_thorsen_ri_se/Documents/Microsoft%20Copilot%20Chat%20Files/convert_openlabel_to_omega.py)
++# Qt binding selection: PyQt5 → PySide6 → PyQt6 (same as your current GUI).
+ try:
+     from PyQt5 import QtCore, QtGui, QtWidgets
+     _QT_API = "PyQt5"
+--- a/src/cosmo/gui/workers.py
++++ b/src/cosmo/gui/workers.py
+@@ -3,7 +3,7 @@
+ 
+ from typing import Callable
+ 
+-# Qt binding selection (same preference order as your current GUI) [1](https://risecloud-my.sharepoint.com/personal/anders_thorsen_ri_se/Documents/Microsoft%20Copilot%20Chat%20Files/convert_openlabel_to_omega.py)
++# Qt binding selection (same preference order as your current GUI)
+ try:
+     from PyQt5 import QtCore
+     _Signal = QtCore.pyqtSignal
+--- a/tests/cli_helpers.py
++++ b/tests/cli_helpers.py
+@@ -21,10 +21,10 @@
+     env.setdefault("MPLBACKEND", "Agg")
+ 
+     if os.name == "nt":
+-        cmd = [sys.executable, "-m", "cosmo.cli.main", *args]  # real entrypoint logic [3](https://risecloud-my.sharepoint.com/personal/anders_thorsen_ri_se/Documents/Microsoft%20Copilot%20Chat%20Files/main.py)
++        cmd = [sys.executable, "-m", "cosmo.cli.main", *args]  # real entrypoint logic
+     else:
+         exe = shutil.which("cosmo")
+-        cmd = [exe, *args] if exe else [sys.executable, "-m", "cosmo.cli.main", *args]  # same entrypoint [3](https://risecloud-my.sharepoint.com/personal/anders_thorsen_ri_se/Documents/Microsoft%20Copilot%20Chat%20Files/main.py)
++        cmd = [exe, *args] if exe else [sys.executable, "-m", "cosmo.cli.main", *args]  # same entrypoint
+ 
+     return subprocess.run(cmd, cwd=str(cwd), capture_output=True, text=True, env=env)
+ 
+--- a/tests/conftest.py
++++ b/tests/conftest.py
+@@ -16,7 +16,7 @@
+     Fallback: if the console script isn't on PATH (rare in CI), run via module entrypoint:
+         python -m cosmo.cli.main <args...>
+ 
+-    NOTE: Never call plain `cosmo` with no args in CI, because cosmo.cli.main defaults to GUI. [2](https://risecloud-my.sharepoint.com/personal/anders_thorsen_ri_se/Documents/Microsoft%20Copilot%20Chat%20Files/main.py)
++    NOTE: Never call plain `cosmo` with no args in CI, because cosmo.cli.main defaults to GUI.
+     """
+     env = dict(os.environ)
+     env.setdefault("MPLBACKEND", "Agg")  # CI already sets this, but keep it deterministic. [1](blob:https://www.microsoft365.com/3377b2c7-ce90-4a5f-bcf4-96fccf281101)
+@@ -26,7 +26,7 @@
+         cmd = [exe, *args]
+     else:
+         # Still the real entrypoint, just executed as a module.
+-        cmd = [os.environ.get("PYTHON", "python"), "-m", "cosmo.cli.main", *args]  # dispatch logic in main.py [2](https://risecloud-my.sharepoint.com/personal/anders_thorsen_ri_se/Documents/Microsoft%20Copilot%20Chat%20Files/main.py)
++        cmd = [os.environ.get("PYTHON", "python"), "-m", "cosmo.cli.main", *args]  # dispatch logic in main.py
+ 
+     return subprocess.run(cmd, cwd=str(cwd), capture_output=True, text=True, env=env)
+ 
+--- a/tests/test_calibration_compute_whitebox.py
++++ b/tests/test_calibration_compute_whitebox.py
+@@ -6,7 +6,7 @@
+ import numpy as np
+ import pytest
+ 
+-from cosmo.calibration.compute import (  # [1](https://risecloud-my.sharepoint.com/personal/anders_thorsen_ri_se/Documents/Microsoft%20Copilot%20Chat%20Files/compute.py)
++from cosmo.calibration.compute import (  #
+     compute_calibration,
+     write_calibration_outputs,
+ )
+@@ -75,7 +75,7 @@
+         fps=30.0,
+         image_width=3840,
+         image_height=2160,
+-        residuals_png_path=str(resid_png),  # optional; may become None on plot errors [1](https://risecloud-my.sharepoint.com/personal/anders_thorsen_ri_se/Documents/Microsoft%20Copilot%20Chat%20Files/compute.py)
++        residuals_png_path=str(resid_png),  # optional; may become None on plot errors
+         overlay_png_path=None,
+         image_path=None,
+         openlabel_path=None,
+@@ -85,7 +85,7 @@
+     assert Path(outs.summary_json_path).is_file()
+ 
+     calib = json.loads(Path(outs.calibration_json_path).read_text(encoding="utf-8"))
+-    # Required keys written by write_calibration_outputs [1](https://risecloud-my.sharepoint.com/personal/anders_thorsen_ri_se/Documents/Microsoft%20Copilot%20Chat%20Files/compute.py)
++    # Required keys written by write_calibration_outputs
+     for k in ("fps", "image_width", "image_height", "homography", "intrinsics", "extrinsics", "default_dimensions_m"):
+         assert k in calib
+     H = calib["homography"]
+@@ -95,7 +95,7 @@
+     for k in ("rmse_m", "inliers_count", "pairs_used", "pixel_points", "world_points_ENU_m", "homography"):
+         assert k in summary
+ 
+-    # Residual plot can be omitted if matplotlib errors; if present, ensure file exists [1](https://risecloud-my.sharepoint.com/personal/anders_thorsen_ri_se/Documents/Microsoft%20Copilot%20Chat%20Files/compute.py)
++    # Residual plot can be omitted if matplotlib errors; if present, ensure file exists
+     if outs.residuals_png_path is not None:
+         assert Path(outs.residuals_png_path).is_file()
+ 
+--- a/tests/test_console_scripts_smoke.py
++++ b/tests/test_console_scripts_smoke.py
+@@ -50,19 +50,19 @@
+     assert cosmo_calibrate, "Expected 'cosmo-calibrate' on PATH or in venv bin dir after install."
+     assert cosmo_gui, "Expected 'cosmo-gui' on PATH or in venv bin dir after install."
+ 
+-    # Always safe: module entrypoint tests real main.py behavior. [3](https://risecloud-my.sharepoint.com/personal/anders_thorsen_ri_se/Documents/Microsoft%20Copilot%20Chat%20Files/main.py)
++    # Always safe: module entrypoint tests real main.py behavior.
+     res = _run([sys.executable, "-m", "cosmo.cli.main", "--version"])
+     assert res.returncode == 0, f"cosmo --version failed.\nSTDOUT:\n{res.stdout}\nSTDERR:\n{res.stderr}"
+     assert res.stdout.strip(), "cosmo --version produced no output."
+ 
+-    # Dispatch help via main.py (convert/calibrate are subcommands). [3](https://risecloud-my.sharepoint.com/personal/anders_thorsen_ri_se/Documents/Microsoft%20Copilot%20Chat%20Files/main.py)
++    # Dispatch help via main.py (convert/calibrate are subcommands).
+     res = _run([sys.executable, "-m", "cosmo.cli.main", "convert", "--help"])
+     assert res.returncode == 0, f"cosmo convert --help failed.\nSTDOUT:\n{res.stdout}\nSTDERR:\n{res.stderr}"
+ 
+     res = _run([sys.executable, "-m", "cosmo.cli.main", "calibrate", "--help"])
+     assert res.returncode == 0, f"cosmo calibrate --help failed.\nSTDOUT:\n{res.stdout}\nSTDERR:\n{res.stderr}"
+ 
+-    # Direct entrypoints: run via module on Windows to avoid blocked .EXE shims. [1](https://risecloud-my.sharepoint.com/personal/anders_thorsen_ri_se/Documents/Microsoft%20Copilot%20Chat%20Files/main.py)[2](https://risecloud-my.sharepoint.com/personal/anders_thorsen_ri_se/Documents/Microsoft%20Copilot%20Chat%20Files/main.py)
++    # Direct entrypoints: run via module on Windows to avoid blocked .EXE shims.
+     if os.name == "nt":
+         res = _run([sys.executable, "-m", "cosmo.cli.convert", "--help"])
+         assert res.returncode == 0, f"python -m cosmo.cli.convert --help failed.\nSTDOUT:\n{res.stdout}\nSTDERR:\n{res.stderr}"
+@@ -76,4 +76,4 @@
+         res = _run([cosmo_calibrate, "--help"])
+         assert res.returncode == 0, f"cosmo-calibrate --help failed.\nSTDOUT:\n{res.stdout}\nSTDERR:\n{res.stderr}"
+ 
+-    # Do NOT execute cosmo-gui in tests: it launches GUI immediately and can fail headless. [3](https://risecloud-my.sharepoint.com/personal/anders_thorsen_ri_se/Documents/Microsoft%20Copilot%20Chat%20Files/main.py)[3](https://risecloud-my.sharepoint.com/personal/anders_thorsen_ri_se/Documents/Microsoft%20Copilot%20Chat%20Files/main.py)
++    # Do NOT execute cosmo-gui in tests: it launches GUI immediately and can fail headless.
+--- a/tests/test_convert_app_e2e_not_smoke.py
++++ b/tests/test_convert_app_e2e_not_smoke.py
+@@ -5,7 +5,7 @@
+ import json
+ from pathlib import Path
+ 
+-from cosmo.app.convert_app import (  # [1](https://risecloud-my.sharepoint.com/personal/anders_thorsen_ri_se/Documents/Microsoft%20Copilot%20Chat%20Files/compute.py)
++from cosmo.app.convert_app import (  #
+     ConvertConfig,
+     run_convert,
+ )
+--- a/tests/test_convert_no_scripts_fallback.py
++++ b/tests/test_convert_no_scripts_fallback.py
+@@ -2,7 +2,7 @@
+ from __future__ import annotations
+ 
+ from cosmo.app.convert_app import (
+-    _get_converter_or_raise,  # internal helper [2](https://risecloud-my.sharepoint.com/personal/anders_thorsen_ri_se/Documents/Microsoft%20Copilot%20Chat%20Files/convert_app.py)
++    _get_converter_or_raise,  # internal helper
+ )
+ 
+ 
+@@ -11,7 +11,7 @@
+         fn = _get_converter_or_raise()
+         assert callable(fn)
+     except RuntimeError as e:
+-        # If it fails, ensure the error message guides the developer correctly. [2](https://risecloud-my.sharepoint.com/personal/anders_thorsen_ri_se/Documents/Microsoft%20Copilot%20Chat%20Files/convert_app.py)
++        # If it fails, ensure the error message guides the developer correctly.
+         msg = str(e)
+         assert "COSMO converter implementation not found" in msg
+         assert "cosmo.converters.openlabel_to_omega" in msg
+--- a/tests/test_core_calibrate_whitebox.py
++++ b/tests/test_core_calibrate_whitebox.py
+@@ -3,7 +3,7 @@
+ import json
+ from pathlib import Path
+ 
+-from cosmo.app.calibrate_app import (  # app layer API [1](https://risecloud-my.sharepoint.com/personal/anders_thorsen_ri_se/Documents/Microsoft%20Copilot%20Chat%20Files/calibrate_app.py)
++from cosmo.app.calibrate_app import (  # app layer API
+     CalibrateConfig,
+     run_calibrate,
+ )
+@@ -34,7 +34,7 @@
+     opendrive = tmp_path / "map.xodr"
+     opendrive.write_text("<OpenDRIVE></OpenDRIVE>", encoding="utf-8")
+ 
+-    # Deterministic run folder: existing out_dir + run_name => out_dir/run_name [1](https://risecloud-my.sharepoint.com/personal/anders_thorsen_ri_se/Documents/Microsoft%20Copilot%20Chat%20Files/calibrate_app.py)
++    # Deterministic run folder: existing out_dir + run_name => out_dir/run_name
+     runs_dir = tmp_path / "runs"
+     runs_dir.mkdir()
+ 
+@@ -55,7 +55,7 @@
+     )
+ 
+     logs: list[str] = []
+-    result = run_calibrate(cfg, log_fn=logs.append)  # same signature used by CLI [1](https://risecloud-my.sharepoint.com/personal/anders_thorsen_ri_se/Documents/Microsoft%20Copilot%20Chat%20Files/calibrate_app.py)
++    result = run_calibrate(cfg, log_fn=logs.append)  # same signature used by CLI
+ 
+     run_dir = Path(result.run_dir)
+     outputs_dir = Path(result.outputs_dir)
+@@ -63,7 +63,7 @@
+     assert outputs_dir == run_dir / "outputs"
+     assert outputs_dir.exists()
+ 
+-    # Output naming is stem-based: <base>_calibration.json etc. [1](https://risecloud-my.sharepoint.com/personal/anders_thorsen_ri_se/Documents/Microsoft%20Copilot%20Chat%20Files/calibrate_app.py)
++    # Output naming is stem-based: <base>_calibration.json etc.
+     calib_path = Path(result.calibration_json_path)
+     assert calib_path.is_file()
+     assert calib_path.name.endswith("_calibration.json")
+@@ -73,15 +73,15 @@
+     H = calib["homography"]
+     assert isinstance(H, list) and len(H) == 3 and all(len(r) == 3 for r in H)
+ 
+-    # Summary JSON should be produced (unless compute/write changes) [1](https://risecloud-my.sharepoint.com/personal/anders_thorsen_ri_se/Documents/Microsoft%20Copilot%20Chat%20Files/calibrate_app.py)
++    # Summary JSON should be produced (unless compute/write changes)
+     if result.summary_json_path:
+         assert Path(result.summary_json_path).is_file()
+ 
+-    # Residual plot is intended but can be None (matplotlib issues), so keep optional. [1](https://risecloud-my.sharepoint.com/personal/anders_thorsen_ri_se/Documents/Microsoft%20Copilot%20Chat%20Files/calibrate_app.py)
++    # Residual plot is intended but can be None (matplotlib issues), so keep optional.
+     if result.residuals_png_path:
+         assert Path(result.residuals_png_path).is_file()
+ 
+-    # No overlay expected because image=None [1](https://risecloud-my.sharepoint.com/personal/anders_thorsen_ri_se/Documents/Microsoft%20Copilot%20Chat%20Files/calibrate_app.py)
++    # No overlay expected because image=None
+     assert result.overlay_png_path is None
+ 
+     # Some logging should occur (useful diagnostic)
+--- a/tests/test_core_convert_whitebox.py
++++ b/tests/test_core_convert_whitebox.py
+@@ -4,7 +4,7 @@
+ import json
+ from pathlib import Path
+ 
+-from cosmo.app.convert_app import (  # app layer API [2](https://risecloud-my.sharepoint.com/personal/anders_thorsen_ri_se/Documents/Microsoft%20Copilot%20Chat%20Files/convert_app.py)
++from cosmo.app.convert_app import (  # app layer API
+     ConvertConfig,
+     run_convert,
+ )
+@@ -31,7 +31,7 @@
+     openlabel_path = tmp_path / "openlabel.json"
+     openlabel_path.write_text(json.dumps(openlabel), encoding="utf-8")
+ 
+-    # Minimal calibration file path (convert_app passes this to converter if provided) [2](https://risecloud-my.sharepoint.com/personal/anders_thorsen_ri_se/Documents/Microsoft%20Copilot%20Chat%20Files/convert_app.py)
++    # Minimal calibration file path (convert_app passes this to converter if provided)
+     calib = {
+         "fps": 30.0,
+         "image_width": 3840,
+@@ -51,7 +51,7 @@
+         calibration=str(calib_path),
+         fps=None,
+         write_csv=True,
+-        write_mcap=False,  # keep core tests independent of optional MCAP deps [2](https://risecloud-my.sharepoint.com/personal/anders_thorsen_ri_se/Documents/Microsoft%20Copilot%20Chat%20Files/convert_app.py)
++        write_mcap=False,  # keep core tests independent of optional MCAP deps
+         swap_xy=False,
+         flip_x=False,
+         flip_y=False,
+@@ -62,7 +62,7 @@
+     )
+ 
+     logs: list[str] = []
+-    result = run_convert(cfg, log_fn=logs.append)  # same signature used by CLI [2](https://risecloud-my.sharepoint.com/personal/anders_thorsen_ri_se/Documents/Microsoft%20Copilot%20Chat%20Files/convert_app.py)
++    result = run_convert(cfg, log_fn=logs.append)  # same signature used by CLI
+ 
+     run_dir = Path(result.run_dir)
+     outputs_dir = Path(result.outputs_dir)
+@@ -70,7 +70,7 @@
+     assert outputs_dir == run_dir / "outputs"
+     assert outputs_dir.exists()
+ 
+-    # csv_path is only set if the file exists (summary filters non-existent files) [2](https://risecloud-my.sharepoint.com/personal/anders_thorsen_ri_se/Documents/Microsoft%20Copilot%20Chat%20Files/convert_app.py)
++    # csv_path is only set if the file exists (summary filters non-existent files)
+     assert result.csv_path is not None
+     csv_path = Path(result.csv_path)
+     assert csv_path.is_file()
+@@ -103,7 +103,7 @@
+         write_mcap=False,
+         out_dir=str(runs_dir),
+         run_name="wb_no_csv",
+-    )  # relies on defaults for other fields [2](https://risecloud-my.sharepoint.com/personal/anders_thorsen_ri_se/Documents/Microsoft%20Copilot%20Chat%20Files/convert_app.py)
++    )  # relies on defaults for other fields
+ 
+     result = run_convert(cfg, log_fn=lambda _: None)
+     assert result.csv_path is None
+--- a/tests/test_integration_mcap_convert_app.py
++++ b/tests/test_integration_mcap_convert_app.py
+@@ -5,7 +5,7 @@
+ 
+ import pytest
+ 
+-from cosmo.app.convert_app import (  # [3](https://risecloud-my.sharepoint.com/personal/anders_thorsen_ri_se/Documents/Microsoft%20Copilot%20Chat%20Files/compute.py)
++from cosmo.app.convert_app import (  #
+     ConvertConfig,
+     run_convert,
+ )
+@@ -20,7 +20,7 @@
+ 
+ 
+ @pytest.mark.integration
+-@pytest.mark.skipif(not _has_betterosi(), reason="betterosi not installed; MCAP integration test skipped")  # [1](https://risecloud-my.sharepoint.com/personal/anders_thorsen_ri_se/Documents/Microsoft%20Copilot%20Chat%20Files/openlabel_to_omega.py)
++@pytest.mark.skipif(not _has_betterosi(), reason="betterosi not installed; MCAP integration test skipped")  #
+ def test_run_convert_app_writes_mcap_and_sets_result_path(tmp_path: Path):
+     # Minimal OpenLABEL
+     openlabel = {
+@@ -36,7 +36,7 @@
+     calib_path = tmp_path / "Calibration.json"
+     calib_path.write_text(json.dumps({"fps": 10.0, "homography": [[1, 0, 0], [0, 1, 0], [0, 0, 1]]}), encoding="utf-8")
+ 
+-    # OpenDRIVE embedded flag in convert_app summary is based on cfg.opendrive [3](https://risecloud-my.sharepoint.com/personal/anders_thorsen_ri_se/Documents/Microsoft%20Copilot%20Chat%20Files/compute.py)
++    # OpenDRIVE embedded flag in convert_app summary is based on cfg.opendrive
+     odr_path = tmp_path / "map.xodr"
+     odr_path.write_text("<OpenDRIVE></OpenDRIVE>", encoding="utf-8")
+ 
+@@ -51,14 +51,14 @@
+         write_mcap=True,
+         out_dir=str(runs_dir),
+         run_name="int_mcap",
+-    )  # config matches app layer [3](https://risecloud-my.sharepoint.com/personal/anders_thorsen_ri_se/Documents/Microsoft%20Copilot%20Chat%20Files/compute.py)
++    )  # config matches app layer
+ 
+     result = run_convert(cfg, log_fn=None)
+ 
+     assert Path(result.run_dir).exists()
+     assert Path(result.outputs_dir).exists()
+ 
+-    # convert_app only sets mcap_path if file exists [3](https://risecloud-my.sharepoint.com/personal/anders_thorsen_ri_se/Documents/Microsoft%20Copilot%20Chat%20Files/compute.py)
++    # convert_app only sets mcap_path if file exists
+     assert result.mcap_path is not None
+     assert Path(result.mcap_path).is_file()
+     assert Path(result.mcap_path).stat().st_size > 0
+--- a/tests/test_integration_mcap_converter.py
++++ b/tests/test_integration_mcap_converter.py
+@@ -6,7 +6,7 @@
+ import pytest
+ 
+ from cosmo.converters.openlabel_to_omega import (
+-    convert_openlabel_to_omega,  # [1](https://risecloud-my.sharepoint.com/personal/anders_thorsen_ri_se/Documents/Microsoft%20Copilot%20Chat%20Files/openlabel_to_omega.py)
++    convert_openlabel_to_omega,  #
+ )
+ 
+ 
+@@ -37,7 +37,7 @@
+ 
+ 
+ @pytest.mark.integration
+-@pytest.mark.skipif(not _has_betterosi(), reason="betterosi not installed; MCAP integration test skipped")  # [1](https://risecloud-my.sharepoint.com/personal/anders_thorsen_ri_se/Documents/Microsoft%20Copilot%20Chat%20Files/openlabel_to_omega.py)
++@pytest.mark.skipif(not _has_betterosi(), reason="betterosi not installed; MCAP integration test skipped")  #
+ def test_converter_writes_mcap_with_ground_truth_and_map(tmp_path: Path):
+     # Minimal OpenLABEL with two frames (ensures multiple GT messages)
+     openlabel = {
+@@ -67,7 +67,7 @@
+         encoding="utf-8",
+     )
+ 
+-    # Provide OpenDRIVE so map embedding path is exercised (ground_truth_map topic) [1](https://risecloud-my.sharepoint.com/personal/anders_thorsen_ri_se/Documents/Microsoft%20Copilot%20Chat%20Files/openlabel_to_omega.py)
++    # Provide OpenDRIVE so map embedding path is exercised (ground_truth_map topic)
+     odr_path = tmp_path / "map.xodr"
+     odr_path.write_text("<OpenDRIVE></OpenDRIVE>", encoding="utf-8")
+ 
+@@ -82,7 +82,7 @@
+         georef_data_path=None,
+         fps_arg=None,
+         write_csv=False,   # focus on MCAP in this integration test
+-        write_mcap=True,   # requires betterosi [1](https://risecloud-my.sharepoint.com/personal/anders_thorsen_ri_se/Documents/Microsoft%20Copilot%20Chat%20Files/openlabel_to_omega.py)
++        write_mcap=True,   # requires betterosi
+         swap_xy=False,
+         flip_x=False,
+         flip_y=False,
+@@ -98,6 +98,6 @@
+     # Optional deeper validation if the `mcap` reader is installed:
+     topics = _try_read_mcap_topics(mcap_path)
+     if topics:
+-        # Converter writes these topics without leading '/' [1](https://risecloud-my.sharepoint.com/personal/anders_thorsen_ri_se/Documents/Microsoft%20Copilot%20Chat%20Files/openlabel_to_omega.py)
++        # Converter writes these topics without leading '/'
+         assert "ground_truth" in topics
+         assert "ground_truth_map" in topics
+--- a/tests/test_integration_mcap_gt_count.py
++++ b/tests/test_integration_mcap_gt_count.py
+@@ -23,7 +23,7 @@
+ 
+ import pytest
+ 
+-from cosmo.app.convert_app import (  # app layer [2](https://risecloud-my.sharepoint.com/personal/anders_thorsen_ri_se/Documents/Microsoft%20Copilot%20Chat%20Files/compute.py)
++from cosmo.app.convert_app import (  # app layer
+     ConvertConfig,
+     run_convert,
+ )
+@@ -62,7 +62,7 @@
+ 
+ 
+ @pytest.mark.integration
+-@pytest.mark.skipif(not _has_betterosi(), reason="betterosi not installed; cannot write MCAP")  # converter depends on it [1](https://risecloud-my.sharepoint.com/personal/anders_thorsen_ri_se/Documents/Microsoft%20Copilot%20Chat%20Files/openlabel_to_omega.py)
++@pytest.mark.skipif(not _has_betterosi(), reason="betterosi not installed; cannot write MCAP")  # converter depends on it
+ @pytest.mark.skipif(not has_mcap_reader(), reason="mcap reader not installed; cannot inspect MCAP")
+ def test_mcap_gt_count_map_once_and_strictly_increasing_log_time(tmp_path: Path):
+     # Create OpenLABEL with a known number of frames.
+@@ -104,7 +104,7 @@
+         encoding="utf-8",
+     )
+ 
+-    # OpenDRIVE included so map is embedded as `ground_truth_map` (written once with log_time=0) [1](https://risecloud-my.sharepoint.com/personal/anders_thorsen_ri_se/Documents/Microsoft%20Copilot%20Chat%20Files/openlabel_to_omega.py)
++    # OpenDRIVE included so map is embedded as `ground_truth_map` (written once with log_time=0)
+     odr_path = tmp_path / "map.xodr"
+     odr_path.write_text("<OpenDRIVE></OpenDRIVE>", encoding="utf-8")
+ 
+@@ -119,10 +119,10 @@
+         write_mcap=True,
+         out_dir=str(runs_dir),
+         run_name="mcap_gt_count",
+-    )  # app layer writes into per-run outputs/ folder [2](https://risecloud-my.sharepoint.com/personal/anders_thorsen_ri_se/Documents/Microsoft%20Copilot%20Chat%20Files/compute.py)
++    )  # app layer writes into per-run outputs/ folder
+ 
+     result = run_convert(cfg, log_fn=None)
+-    assert result.mcap_path, "Expected mcap_path to be set when MCAP is written"  # app layer sets only if file exists [2](https://risecloud-my.sharepoint.com/personal/anders_thorsen_ri_se/Documents/Microsoft%20Copilot%20Chat%20Files/compute.py)
++    assert result.mcap_path, "Expected mcap_path to be set when MCAP is written"  # app layer sets only if file exists
+ 
+     mcap_path = assert_mcap_nonempty(result.mcap_path)
+ 
+@@ -130,11 +130,11 @@
+     gt_times = _collect_topic_log_times(mcap_path, "ground_truth")
+     assert len(gt_times) == len(frame_ids), f"Expected {len(frame_ids)} ground_truth messages, got {len(gt_times)}"
+ 
+-    # 2) Map message written exactly once at log_time=0 (converter writes once) [1](https://risecloud-my.sharepoint.com/personal/anders_thorsen_ri_se/Documents/Microsoft%20Copilot%20Chat%20Files/openlabel_to_omega.py)
++    # 2) Map message written exactly once at log_time=0 (converter writes once)
+     map_times = _collect_topic_log_times(mcap_path, "ground_truth_map")
+     assert len(map_times) == 1, f"Expected exactly 1 ground_truth_map message, got {len(map_times)}"
+     assert map_times[0] == 0, f"Expected ground_truth_map log_time=0, got {map_times[0]}"
+ 
+-    # 3) GroundTruth log_time strictly increasing (converter uses log_time=total_nanos) [1](https://risecloud-my.sharepoint.com/personal/anders_thorsen_ri_se/Documents/Microsoft%20Copilot%20Chat%20Files/openlabel_to_omega.py)
++    # 3) GroundTruth log_time strictly increasing (converter uses log_time=total_nanos)
+     assert gt_times == sorted(gt_times), f"ground_truth log_time not non-decreasing: {gt_times}"
+     assert all(b > a for a, b in zip(gt_times, gt_times[1:])), f"ground_truth log_time not strictly increasing: {gt_times}"
+--- a/tests/test_main_dispatch.py
++++ b/tests/test_main_dispatch.py
+@@ -14,5 +14,5 @@
+         text=True,
+         env={**os.environ, "MPLBACKEND": "Agg"},
+     )
+-    assert res.returncode == 0  # main.py returns 0 on --version [1](https://risecloud-my.sharepoint.com/personal/anders_thorsen_ri_se/Documents/Microsoft%20Copilot%20Chat%20Files/main.py)
+-    assert res.stdout.strip()  # prints version string [1](https://risecloud-my.sharepoint.com/personal/anders_thorsen_ri_se/Documents/Microsoft%20Copilot%20Chat%20Files/main.py)
++    assert res.returncode == 0  # main.py returns 0 on --version
++    assert res.stdout.strip()  # prints version string
+--- a/tests/test_openlabel_to_omega_whitebox.py
++++ b/tests/test_openlabel_to_omega_whitebox.py
+@@ -6,7 +6,7 @@
+ 
+ import numpy as np
+ 
+-from cosmo.converters.openlabel_to_omega import (  # [2](https://risecloud-my.sharepoint.com/personal/anders_thorsen_ri_se/Documents/Microsoft%20Copilot%20Chat%20Files/openlabel_to_omega.py)
++from cosmo.converters.openlabel_to_omega import (  #
+     convert_openlabel_to_omega,
+     load_alignment,
+     parse_openlabel,
+@@ -82,7 +82,7 @@
+         georef_data_path=None,
+         fps_arg=None,
+         write_csv=True,
+-        write_mcap=False,  # ensure no betterosi dependency [2](https://risecloud-my.sharepoint.com/personal/anders_thorsen_ri_se/Documents/Microsoft%20Copilot%20Chat%20Files/openlabel_to_omega.py)
++        write_mcap=False,  # ensure no betterosi dependency
+         swap_xy=False,
+         flip_x=False,
+         flip_y=False,
+@@ -96,11 +96,11 @@
+ 
+     with csv_path.open(newline="", encoding="utf-8") as f:
+         reader = csv.DictReader(f)
+-        # Columns defined in module [2](https://risecloud-my.sharepoint.com/personal/anders_thorsen_ri_se/Documents/Microsoft%20Copilot%20Chat%20Files/openlabel_to_omega.py)
++        # Columns defined in module
+         for col in ("total_nanos", "idx", "x", "y", "yaw", "type_name", "subtype_name", "role_name"):
+             assert col in (reader.fieldnames or [])
+         rows = list(reader)
+         assert len(rows) >= 2
+-        # Ensure time is non-decreasing (rows are sorted by total_nanos) [2](https://risecloud-my.sharepoint.com/personal/anders_thorsen_ri_se/Documents/Microsoft%20Copilot%20Chat%20Files/openlabel_to_omega.py)
++        # Ensure time is non-decreasing (rows are sorted by total_nanos)
+         times = [int(r["total_nanos"]) for r in rows]
+         assert times == sorted(times)
diff --git a/cosmo_required_fixes.patch:Zone.Identifier b/cosmo_required_fixes.patch:Zone.Identifier
new file mode 100644
index 0000000000000000000000000000000000000000..d6c1ec682968c796b9f5e9e080cc6f674b57c766
GIT binary patch
literal 25
dcma!!%Fjy;DN4*MPD?F{<>dl#JyUFr831@K2x<TT

literal 0
HcmV?d00001

diff --git a/docs/getting-started/quickstart.md b/docs/getting-started/quickstart.md
index c40dfd5..5fe42e7 100644
--- a/docs/getting-started/quickstart.md
+++ b/docs/getting-started/quickstart.md
@@ -10,17 +10,16 @@ cosmo
 cosmo gui
 ```
 
-Development shortcut (either of):
+Use the installed console script:
 
 ```bash
-python run_gui.py # Start GUI
-python run_cosmo.py gui # Same behaviour as cosmo (when installed)
-cosmo.cmd gui # Same behaviour in Windows cmd termial as cosmo (when installed)
-cosmo.ps1 gui # Same behaviour in Windows PowerShell termial as cosmo (when installed)
+cosmo gui
+# or simply:
+cosmo
 ```
 ---
 ## CLI
-> During development `cosmo ...` can be replaced with `python run_cosmo ...`, `cosmo.exe ...` or `cosmo.ps1 ...` without needing to install cosmo, e.g., `python run_cosmo.py convert ...`. To install for development use `uv sync --group dev` or `pip install -e . --group dev`.
+> For development, install the package first (for example `uv sync --group dev` or `pip install -e . --group dev`) and then use the `cosmo ...` console script.
 ---
 ### Convert (recommended: ORBIT georef)
 
diff --git a/src/cosmo/converters/openlabel_to_omega.py b/src/cosmo/converters/openlabel_to_omega.py
index d4e4cb9..baf713b 100644
--- a/src/cosmo/converters/openlabel_to_omega.py
+++ b/src/cosmo/converters/openlabel_to_omega.py
@@ -721,7 +721,7 @@ def _collect_all_dims() -> Dict[str, Tuple[float, float, float]]:
     # ----------------------------
     # IMPORTANT:
     # Use betterosi.Writer as a context manager to ensure MCAP footer/summary are finalized properly. [1](https://deepwiki.com/ika-rwth-aachen/omega-prime/3.1-loading-and-saving-recordings)[4](https://ika-rwth-aachen.github.io/omega-prime/notebooks/tutorial/)
-    # Also write topic names without leading "/" to match common omega-prime usage. [3](https://risecloud-my.sharepoint.com/personal/anders_thorsen_ri_se/Documents/Microsoft%20Copilot%20Chat%20Files/convert_app.py)[2](https://risecloud-my.sharepoint.com/personal/anders_thorsen_ri_se/Documents/Microsoft%20Copilot%20Chat%20Files/openlabel_to_omega.py)
+    # Also write topic names without leading "/" to match common omega-prime usage.
 
     def _write_map(writer_mcap):
         if odr_path and os.path.isfile(odr_path):
@@ -752,7 +752,7 @@ def _write_ground_truth(writer_mcap, t_sec: float, total_nanos: int, moving_obje
             gt.proj_string = _gt_proj_string
         if _gt_country_code:
             gt.country_code = _gt_country_code
-        # Provide log_time explicitly; readers often build indices from it. [4](https://ika-rwth-aachen.github.io/omega-prime/notebooks/tutorial/)[3](https://risecloud-my.sharepoint.com/personal/anders_thorsen_ri_se/Documents/Microsoft%20Copilot%20Chat%20Files/convert_app.py)
+        # Provide log_time explicitly; readers often build indices from it. [4](https://ika-rwth-aachen.github.io/omega-prime/notebooks/tutorial/)
         writer_mcap.add(gt, topic="ground_truth", log_time=total_nanos)
 
     # If MCAP enabled, write with context manager; else only build CSV rows
diff --git a/src/cosmo/gui/main_window.py b/src/cosmo/gui/main_window.py
index a462d4e..8e99ddc 100644
--- a/src/cosmo/gui/main_window.py
+++ b/src/cosmo/gui/main_window.py
@@ -9,7 +9,7 @@
 from pathlib import Path
 from typing import Optional
 
-# Qt binding selection: PyQt5 → PySide6 → PyQt6 (same as your current GUI). [1](https://risecloud-my.sharepoint.com/personal/anders_thorsen_ri_se/Documents/Microsoft%20Copilot%20Chat%20Files/convert_openlabel_to_omega.py)
+# Qt binding selection: PyQt5 → PySide6 → PyQt6 (same as your current GUI).
 try:
     from PyQt5 import QtCore, QtGui, QtWidgets
     _QT_API = "PyQt5"
diff --git a/src/cosmo/gui/workers.py b/src/cosmo/gui/workers.py
index 16ad7a2..a884056 100644
--- a/src/cosmo/gui/workers.py
+++ b/src/cosmo/gui/workers.py
@@ -3,7 +3,7 @@
 
 from typing import Callable
 
-# Qt binding selection (same preference order as your current GUI) [1](https://risecloud-my.sharepoint.com/personal/anders_thorsen_ri_se/Documents/Microsoft%20Copilot%20Chat%20Files/convert_openlabel_to_omega.py)
+# Qt binding selection (same preference order as your current GUI)
 try:
     from PyQt5 import QtCore
     _Signal = QtCore.pyqtSignal
diff --git a/tests/cli_helpers.py b/tests/cli_helpers.py
index 8576204..5d8643c 100644
--- a/tests/cli_helpers.py
+++ b/tests/cli_helpers.py
@@ -21,10 +21,10 @@ def run_cosmo(args: list[str], *, cwd: Path) -> subprocess.CompletedProcess[str]
     env.setdefault("MPLBACKEND", "Agg")
 
     if os.name == "nt":
-        cmd = [sys.executable, "-m", "cosmo.cli.main", *args]  # real entrypoint logic [3](https://risecloud-my.sharepoint.com/personal/anders_thorsen_ri_se/Documents/Microsoft%20Copilot%20Chat%20Files/main.py)
+        cmd = [sys.executable, "-m", "cosmo.cli.main", *args]  # real entrypoint logic
     else:
         exe = shutil.which("cosmo")
-        cmd = [exe, *args] if exe else [sys.executable, "-m", "cosmo.cli.main", *args]  # same entrypoint [3](https://risecloud-my.sharepoint.com/personal/anders_thorsen_ri_se/Documents/Microsoft%20Copilot%20Chat%20Files/main.py)
+        cmd = [exe, *args] if exe else [sys.executable, "-m", "cosmo.cli.main", *args]  # same entrypoint
 
     return subprocess.run(cmd, cwd=str(cwd), capture_output=True, text=True, env=env)
 
diff --git a/tests/conftest.py b/tests/conftest.py
index 68388c3..4f94ab9 100644
--- a/tests/conftest.py
+++ b/tests/conftest.py
@@ -16,7 +16,7 @@ def run_cosmo(args: list[str], *, cwd: Path) -> subprocess.CompletedProcess[str]
     Fallback: if the console script isn't on PATH (rare in CI), run via module entrypoint:
         python -m cosmo.cli.main <args...>
 
-    NOTE: Never call plain `cosmo` with no args in CI, because cosmo.cli.main defaults to GUI. [2](https://risecloud-my.sharepoint.com/personal/anders_thorsen_ri_se/Documents/Microsoft%20Copilot%20Chat%20Files/main.py)
+    NOTE: Never call plain `cosmo` with no args in CI, because cosmo.cli.main defaults to GUI.
     """
     env = dict(os.environ)
     env.setdefault("MPLBACKEND", "Agg")  # CI already sets this, but keep it deterministic. [1](blob:https://www.microsoft365.com/3377b2c7-ce90-4a5f-bcf4-96fccf281101)
@@ -26,7 +26,7 @@ def run_cosmo(args: list[str], *, cwd: Path) -> subprocess.CompletedProcess[str]
         cmd = [exe, *args]
     else:
         # Still the real entrypoint, just executed as a module.
-        cmd = [os.environ.get("PYTHON", "python"), "-m", "cosmo.cli.main", *args]  # dispatch logic in main.py [2](https://risecloud-my.sharepoint.com/personal/anders_thorsen_ri_se/Documents/Microsoft%20Copilot%20Chat%20Files/main.py)
+        cmd = [os.environ.get("PYTHON", "python"), "-m", "cosmo.cli.main", *args]  # dispatch logic in main.py
 
     return subprocess.run(cmd, cwd=str(cwd), capture_output=True, text=True, env=env)
 
diff --git a/tests/test_calibration_compute_whitebox.py b/tests/test_calibration_compute_whitebox.py
index 0a54fc0..48f87c8 100644
--- a/tests/test_calibration_compute_whitebox.py
+++ b/tests/test_calibration_compute_whitebox.py
@@ -6,7 +6,7 @@
 import numpy as np
 import pytest
 
-from cosmo.calibration.compute import (  # [1](https://risecloud-my.sharepoint.com/personal/anders_thorsen_ri_se/Documents/Microsoft%20Copilot%20Chat%20Files/compute.py)
+from cosmo.calibration.compute import (  #
     compute_calibration,
     write_calibration_outputs,
 )
@@ -75,7 +75,7 @@ def test_write_calibration_outputs_writes_expected_json_schema(tmp_path: Path):
         fps=30.0,
         image_width=3840,
         image_height=2160,
-        residuals_png_path=str(resid_png),  # optional; may become None on plot errors [1](https://risecloud-my.sharepoint.com/personal/anders_thorsen_ri_se/Documents/Microsoft%20Copilot%20Chat%20Files/compute.py)
+        residuals_png_path=str(resid_png),  # optional; may become None on plot errors
         overlay_png_path=None,
         image_path=None,
         openlabel_path=None,
@@ -85,7 +85,7 @@ def test_write_calibration_outputs_writes_expected_json_schema(tmp_path: Path):
     assert Path(outs.summary_json_path).is_file()
 
     calib = json.loads(Path(outs.calibration_json_path).read_text(encoding="utf-8"))
-    # Required keys written by write_calibration_outputs [1](https://risecloud-my.sharepoint.com/personal/anders_thorsen_ri_se/Documents/Microsoft%20Copilot%20Chat%20Files/compute.py)
+    # Required keys written by write_calibration_outputs
     for k in ("fps", "image_width", "image_height", "homography", "intrinsics", "extrinsics", "default_dimensions_m"):
         assert k in calib
     H = calib["homography"]
@@ -95,7 +95,7 @@ def test_write_calibration_outputs_writes_expected_json_schema(tmp_path: Path):
     for k in ("rmse_m", "inliers_count", "pairs_used", "pixel_points", "world_points_ENU_m", "homography"):
         assert k in summary
 
-    # Residual plot can be omitted if matplotlib errors; if present, ensure file exists [1](https://risecloud-my.sharepoint.com/personal/anders_thorsen_ri_se/Documents/Microsoft%20Copilot%20Chat%20Files/compute.py)
+    # Residual plot can be omitted if matplotlib errors; if present, ensure file exists
     if outs.residuals_png_path is not None:
         assert Path(outs.residuals_png_path).is_file()
 
diff --git a/tests/test_console_scripts_smoke.py b/tests/test_console_scripts_smoke.py
index c2c94b9..6527104 100644
--- a/tests/test_console_scripts_smoke.py
+++ b/tests/test_console_scripts_smoke.py
@@ -50,19 +50,19 @@ def test_console_scripts_exist_and_help_works():
     assert cosmo_calibrate, "Expected 'cosmo-calibrate' on PATH or in venv bin dir after install."
     assert cosmo_gui, "Expected 'cosmo-gui' on PATH or in venv bin dir after install."
 
-    # Always safe: module entrypoint tests real main.py behavior. [3](https://risecloud-my.sharepoint.com/personal/anders_thorsen_ri_se/Documents/Microsoft%20Copilot%20Chat%20Files/main.py)
+    # Always safe: module entrypoint tests real main.py behavior.
     res = _run([sys.executable, "-m", "cosmo.cli.main", "--version"])
     assert res.returncode == 0, f"cosmo --version failed.\nSTDOUT:\n{res.stdout}\nSTDERR:\n{res.stderr}"
     assert res.stdout.strip(), "cosmo --version produced no output."
 
-    # Dispatch help via main.py (convert/calibrate are subcommands). [3](https://risecloud-my.sharepoint.com/personal/anders_thorsen_ri_se/Documents/Microsoft%20Copilot%20Chat%20Files/main.py)
+    # Dispatch help via main.py (convert/calibrate are subcommands).
     res = _run([sys.executable, "-m", "cosmo.cli.main", "convert", "--help"])
     assert res.returncode == 0, f"cosmo convert --help failed.\nSTDOUT:\n{res.stdout}\nSTDERR:\n{res.stderr}"
 
     res = _run([sys.executable, "-m", "cosmo.cli.main", "calibrate", "--help"])
     assert res.returncode == 0, f"cosmo calibrate --help failed.\nSTDOUT:\n{res.stdout}\nSTDERR:\n{res.stderr}"
 
-    # Direct entrypoints: run via module on Windows to avoid blocked .EXE shims. [1](https://risecloud-my.sharepoint.com/personal/anders_thorsen_ri_se/Documents/Microsoft%20Copilot%20Chat%20Files/main.py)[2](https://risecloud-my.sharepoint.com/personal/anders_thorsen_ri_se/Documents/Microsoft%20Copilot%20Chat%20Files/main.py)
+    # Direct entrypoints: run via module on Windows to avoid blocked .EXE shims.
     if os.name == "nt":
         res = _run([sys.executable, "-m", "cosmo.cli.convert", "--help"])
         assert res.returncode == 0, f"python -m cosmo.cli.convert --help failed.\nSTDOUT:\n{res.stdout}\nSTDERR:\n{res.stderr}"
@@ -76,4 +76,4 @@ def test_console_scripts_exist_and_help_works():
         res = _run([cosmo_calibrate, "--help"])
         assert res.returncode == 0, f"cosmo-calibrate --help failed.\nSTDOUT:\n{res.stdout}\nSTDERR:\n{res.stderr}"
 
-    # Do NOT execute cosmo-gui in tests: it launches GUI immediately and can fail headless. [3](https://risecloud-my.sharepoint.com/personal/anders_thorsen_ri_se/Documents/Microsoft%20Copilot%20Chat%20Files/main.py)[3](https://risecloud-my.sharepoint.com/personal/anders_thorsen_ri_se/Documents/Microsoft%20Copilot%20Chat%20Files/main.py)
+    # Do NOT execute cosmo-gui in tests: it launches GUI immediately and can fail headless.
diff --git a/tests/test_convert_app_e2e_not_smoke.py b/tests/test_convert_app_e2e_not_smoke.py
index d5ce9e1..bfa902f 100644
--- a/tests/test_convert_app_e2e_not_smoke.py
+++ b/tests/test_convert_app_e2e_not_smoke.py
@@ -5,7 +5,7 @@
 import json
 from pathlib import Path
 
-from cosmo.app.convert_app import (  # [1](https://risecloud-my.sharepoint.com/personal/anders_thorsen_ri_se/Documents/Microsoft%20Copilot%20Chat%20Files/compute.py)
+from cosmo.app.convert_app import (  #
     ConvertConfig,
     run_convert,
 )
diff --git a/tests/test_convert_no_scripts_fallback.py b/tests/test_convert_no_scripts_fallback.py
index fa60d78..6e2d9e1 100644
--- a/tests/test_convert_no_scripts_fallback.py
+++ b/tests/test_convert_no_scripts_fallback.py
@@ -2,7 +2,7 @@
 from __future__ import annotations
 
 from cosmo.app.convert_app import (
-    _get_converter_or_raise,  # internal helper [2](https://risecloud-my.sharepoint.com/personal/anders_thorsen_ri_se/Documents/Microsoft%20Copilot%20Chat%20Files/convert_app.py)
+    _get_converter_or_raise,  # internal helper
 )
 
 
@@ -11,7 +11,7 @@ def test_converter_import_has_clear_error_message():
         fn = _get_converter_or_raise()
         assert callable(fn)
     except RuntimeError as e:
-        # If it fails, ensure the error message guides the developer correctly. [2](https://risecloud-my.sharepoint.com/personal/anders_thorsen_ri_se/Documents/Microsoft%20Copilot%20Chat%20Files/convert_app.py)
+        # If it fails, ensure the error message guides the developer correctly.
         msg = str(e)
         assert "COSMO converter implementation not found" in msg
         assert "cosmo.converters.openlabel_to_omega" in msg
diff --git a/tests/test_core_calibrate_whitebox.py b/tests/test_core_calibrate_whitebox.py
index 570a3d6..712c509 100644
--- a/tests/test_core_calibrate_whitebox.py
+++ b/tests/test_core_calibrate_whitebox.py
@@ -3,7 +3,7 @@
 import json
 from pathlib import Path
 
-from cosmo.app.calibrate_app import (  # app layer API [1](https://risecloud-my.sharepoint.com/personal/anders_thorsen_ri_se/Documents/Microsoft%20Copilot%20Chat%20Files/calibrate_app.py)
+from cosmo.app.calibrate_app import (  # app layer API
     CalibrateConfig,
     run_calibrate,
 )
@@ -34,7 +34,7 @@ def test_run_calibrate_writes_stem_based_outputs(tmp_path: Path):
     opendrive = tmp_path / "map.xodr"
     opendrive.write_text("<OpenDRIVE></OpenDRIVE>", encoding="utf-8")
 
-    # Deterministic run folder: existing out_dir + run_name => out_dir/run_name [1](https://risecloud-my.sharepoint.com/personal/anders_thorsen_ri_se/Documents/Microsoft%20Copilot%20Chat%20Files/calibrate_app.py)
+    # Deterministic run folder: existing out_dir + run_name => out_dir/run_name
     runs_dir = tmp_path / "runs"
     runs_dir.mkdir()
 
@@ -55,7 +55,7 @@ def test_run_calibrate_writes_stem_based_outputs(tmp_path: Path):
     )
 
     logs: list[str] = []
-    result = run_calibrate(cfg, log_fn=logs.append)  # same signature used by CLI [1](https://risecloud-my.sharepoint.com/personal/anders_thorsen_ri_se/Documents/Microsoft%20Copilot%20Chat%20Files/calibrate_app.py)
+    result = run_calibrate(cfg, log_fn=logs.append)  # same signature used by CLI
 
     run_dir = Path(result.run_dir)
     outputs_dir = Path(result.outputs_dir)
@@ -63,7 +63,7 @@ def test_run_calibrate_writes_stem_based_outputs(tmp_path: Path):
     assert outputs_dir == run_dir / "outputs"
     assert outputs_dir.exists()
 
-    # Output naming is stem-based: <base>_calibration.json etc. [1](https://risecloud-my.sharepoint.com/personal/anders_thorsen_ri_se/Documents/Microsoft%20Copilot%20Chat%20Files/calibrate_app.py)
+    # Output naming is stem-based: <base>_calibration.json etc.
     calib_path = Path(result.calibration_json_path)
     assert calib_path.is_file()
     assert calib_path.name.endswith("_calibration.json")
@@ -73,15 +73,15 @@ def test_run_calibrate_writes_stem_based_outputs(tmp_path: Path):
     H = calib["homography"]
     assert isinstance(H, list) and len(H) == 3 and all(len(r) == 3 for r in H)
 
-    # Summary JSON should be produced (unless compute/write changes) [1](https://risecloud-my.sharepoint.com/personal/anders_thorsen_ri_se/Documents/Microsoft%20Copilot%20Chat%20Files/calibrate_app.py)
+    # Summary JSON should be produced (unless compute/write changes)
     if result.summary_json_path:
         assert Path(result.summary_json_path).is_file()
 
-    # Residual plot is intended but can be None (matplotlib issues), so keep optional. [1](https://risecloud-my.sharepoint.com/personal/anders_thorsen_ri_se/Documents/Microsoft%20Copilot%20Chat%20Files/calibrate_app.py)
+    # Residual plot is intended but can be None (matplotlib issues), so keep optional.
     if result.residuals_png_path:
         assert Path(result.residuals_png_path).is_file()
 
-    # No overlay expected because image=None [1](https://risecloud-my.sharepoint.com/personal/anders_thorsen_ri_se/Documents/Microsoft%20Copilot%20Chat%20Files/calibrate_app.py)
+    # No overlay expected because image=None
     assert result.overlay_png_path is None
 
     # Some logging should occur (useful diagnostic)
diff --git a/tests/test_core_convert_whitebox.py b/tests/test_core_convert_whitebox.py
index 9226017..c2fd688 100644
--- a/tests/test_core_convert_whitebox.py
+++ b/tests/test_core_convert_whitebox.py
@@ -4,7 +4,7 @@
 import json
 from pathlib import Path
 
-from cosmo.app.convert_app import (  # app layer API [2](https://risecloud-my.sharepoint.com/personal/anders_thorsen_ri_se/Documents/Microsoft%20Copilot%20Chat%20Files/convert_app.py)
+from cosmo.app.convert_app import (  # app layer API
     ConvertConfig,
     run_convert,
 )
@@ -31,7 +31,7 @@ def test_run_convert_writes_csv_and_sets_csv_path(tmp_path: Path):
     openlabel_path = tmp_path / "openlabel.json"
     openlabel_path.write_text(json.dumps(openlabel), encoding="utf-8")
 
-    # Minimal calibration file path (convert_app passes this to converter if provided) [2](https://risecloud-my.sharepoint.com/personal/anders_thorsen_ri_se/Documents/Microsoft%20Copilot%20Chat%20Files/convert_app.py)
+    # Minimal calibration file path (convert_app passes this to converter if provided)
     calib = {
         "fps": 30.0,
         "image_width": 3840,
@@ -51,7 +51,7 @@ def test_run_convert_writes_csv_and_sets_csv_path(tmp_path: Path):
         calibration=str(calib_path),
         fps=None,
         write_csv=True,
-        write_mcap=False,  # keep core tests independent of optional MCAP deps [2](https://risecloud-my.sharepoint.com/personal/anders_thorsen_ri_se/Documents/Microsoft%20Copilot%20Chat%20Files/convert_app.py)
+        write_mcap=False,  # keep core tests independent of optional MCAP deps
         swap_xy=False,
         flip_x=False,
         flip_y=False,
@@ -62,7 +62,7 @@ def test_run_convert_writes_csv_and_sets_csv_path(tmp_path: Path):
     )
 
     logs: list[str] = []
-    result = run_convert(cfg, log_fn=logs.append)  # same signature used by CLI [2](https://risecloud-my.sharepoint.com/personal/anders_thorsen_ri_se/Documents/Microsoft%20Copilot%20Chat%20Files/convert_app.py)
+    result = run_convert(cfg, log_fn=logs.append)  # same signature used by CLI
 
     run_dir = Path(result.run_dir)
     outputs_dir = Path(result.outputs_dir)
@@ -70,7 +70,7 @@ def test_run_convert_writes_csv_and_sets_csv_path(tmp_path: Path):
     assert outputs_dir == run_dir / "outputs"
     assert outputs_dir.exists()
 
-    # csv_path is only set if the file exists (summary filters non-existent files) [2](https://risecloud-my.sharepoint.com/personal/anders_thorsen_ri_se/Documents/Microsoft%20Copilot%20Chat%20Files/convert_app.py)
+    # csv_path is only set if the file exists (summary filters non-existent files)
     assert result.csv_path is not None
     csv_path = Path(result.csv_path)
     assert csv_path.is_file()
@@ -103,7 +103,7 @@ def test_run_convert_no_csv_results_in_none_csv_path(tmp_path: Path):
         write_mcap=False,
         out_dir=str(runs_dir),
         run_name="wb_no_csv",
-    )  # relies on defaults for other fields [2](https://risecloud-my.sharepoint.com/personal/anders_thorsen_ri_se/Documents/Microsoft%20Copilot%20Chat%20Files/convert_app.py)
+    )  # relies on defaults for other fields
 
     result = run_convert(cfg, log_fn=lambda _: None)
     assert result.csv_path is None
diff --git a/tests/test_integration_mcap_convert_app.py b/tests/test_integration_mcap_convert_app.py
index 625494f..b181215 100644
--- a/tests/test_integration_mcap_convert_app.py
+++ b/tests/test_integration_mcap_convert_app.py
@@ -5,7 +5,7 @@
 
 import pytest
 
-from cosmo.app.convert_app import (  # [3](https://risecloud-my.sharepoint.com/personal/anders_thorsen_ri_se/Documents/Microsoft%20Copilot%20Chat%20Files/compute.py)
+from cosmo.app.convert_app import (  #
     ConvertConfig,
     run_convert,
 )
@@ -20,7 +20,7 @@ def _has_betterosi() -> bool:
 
 
 @pytest.mark.integration
-@pytest.mark.skipif(not _has_betterosi(), reason="betterosi not installed; MCAP integration test skipped")  # [1](https://risecloud-my.sharepoint.com/personal/anders_thorsen_ri_se/Documents/Microsoft%20Copilot%20Chat%20Files/openlabel_to_omega.py)
+@pytest.mark.skipif(not _has_betterosi(), reason="betterosi not installed; MCAP integration test skipped")  #
 def test_run_convert_app_writes_mcap_and_sets_result_path(tmp_path: Path):
     # Minimal OpenLABEL
     openlabel = {
@@ -36,7 +36,7 @@ def test_run_convert_app_writes_mcap_and_sets_result_path(tmp_path: Path):
     calib_path = tmp_path / "Calibration.json"
     calib_path.write_text(json.dumps({"fps": 10.0, "homography": [[1, 0, 0], [0, 1, 0], [0, 0, 1]]}), encoding="utf-8")
 
-    # OpenDRIVE embedded flag in convert_app summary is based on cfg.opendrive [3](https://risecloud-my.sharepoint.com/personal/anders_thorsen_ri_se/Documents/Microsoft%20Copilot%20Chat%20Files/compute.py)
+    # OpenDRIVE embedded flag in convert_app summary is based on cfg.opendrive
     odr_path = tmp_path / "map.xodr"
     odr_path.write_text("<OpenDRIVE></OpenDRIVE>", encoding="utf-8")
 
@@ -51,14 +51,14 @@ def test_run_convert_app_writes_mcap_and_sets_result_path(tmp_path: Path):
         write_mcap=True,
         out_dir=str(runs_dir),
         run_name="int_mcap",
-    )  # config matches app layer [3](https://risecloud-my.sharepoint.com/personal/anders_thorsen_ri_se/Documents/Microsoft%20Copilot%20Chat%20Files/compute.py)
+    )  # config matches app layer
 
     result = run_convert(cfg, log_fn=None)
 
     assert Path(result.run_dir).exists()
     assert Path(result.outputs_dir).exists()
 
-    # convert_app only sets mcap_path if file exists [3](https://risecloud-my.sharepoint.com/personal/anders_thorsen_ri_se/Documents/Microsoft%20Copilot%20Chat%20Files/compute.py)
+    # convert_app only sets mcap_path if file exists
     assert result.mcap_path is not None
     assert Path(result.mcap_path).is_file()
     assert Path(result.mcap_path).stat().st_size > 0
diff --git a/tests/test_integration_mcap_converter.py b/tests/test_integration_mcap_converter.py
index eab2a48..a770f68 100644
--- a/tests/test_integration_mcap_converter.py
+++ b/tests/test_integration_mcap_converter.py
@@ -6,7 +6,7 @@
 import pytest
 
 from cosmo.converters.openlabel_to_omega import (
-    convert_openlabel_to_omega,  # [1](https://risecloud-my.sharepoint.com/personal/anders_thorsen_ri_se/Documents/Microsoft%20Copilot%20Chat%20Files/openlabel_to_omega.py)
+    convert_openlabel_to_omega,  #
 )
 
 
@@ -37,7 +37,7 @@ def _try_read_mcap_topics(mcap_path: Path) -> set[str]:
 
 
 @pytest.mark.integration
-@pytest.mark.skipif(not _has_betterosi(), reason="betterosi not installed; MCAP integration test skipped")  # [1](https://risecloud-my.sharepoint.com/personal/anders_thorsen_ri_se/Documents/Microsoft%20Copilot%20Chat%20Files/openlabel_to_omega.py)
+@pytest.mark.skipif(not _has_betterosi(), reason="betterosi not installed; MCAP integration test skipped")  #
 def test_converter_writes_mcap_with_ground_truth_and_map(tmp_path: Path):
     # Minimal OpenLABEL with two frames (ensures multiple GT messages)
     openlabel = {
@@ -67,7 +67,7 @@ def test_converter_writes_mcap_with_ground_truth_and_map(tmp_path: Path):
         encoding="utf-8",
     )
 
-    # Provide OpenDRIVE so map embedding path is exercised (ground_truth_map topic) [1](https://risecloud-my.sharepoint.com/personal/anders_thorsen_ri_se/Documents/Microsoft%20Copilot%20Chat%20Files/openlabel_to_omega.py)
+    # Provide OpenDRIVE so map embedding path is exercised (ground_truth_map topic)
     odr_path = tmp_path / "map.xodr"
     odr_path.write_text("<OpenDRIVE></OpenDRIVE>", encoding="utf-8")
 
@@ -82,7 +82,7 @@ def test_converter_writes_mcap_with_ground_truth_and_map(tmp_path: Path):
         georef_data_path=None,
         fps_arg=None,
         write_csv=False,   # focus on MCAP in this integration test
-        write_mcap=True,   # requires betterosi [1](https://risecloud-my.sharepoint.com/personal/anders_thorsen_ri_se/Documents/Microsoft%20Copilot%20Chat%20Files/openlabel_to_omega.py)
+        write_mcap=True,   # requires betterosi
         swap_xy=False,
         flip_x=False,
         flip_y=False,
@@ -98,6 +98,6 @@ def test_converter_writes_mcap_with_ground_truth_and_map(tmp_path: Path):
     # Optional deeper validation if the `mcap` reader is installed:
     topics = _try_read_mcap_topics(mcap_path)
     if topics:
-        # Converter writes these topics without leading '/' [1](https://risecloud-my.sharepoint.com/personal/anders_thorsen_ri_se/Documents/Microsoft%20Copilot%20Chat%20Files/openlabel_to_omega.py)
+        # Converter writes these topics without leading '/'
         assert "ground_truth" in topics
         assert "ground_truth_map" in topics
diff --git a/tests/test_integration_mcap_gt_count.py b/tests/test_integration_mcap_gt_count.py
index 7d7d2e4..fffca3c 100644
--- a/tests/test_integration_mcap_gt_count.py
+++ b/tests/test_integration_mcap_gt_count.py
@@ -23,7 +23,7 @@
 
 import pytest
 
-from cosmo.app.convert_app import (  # app layer [2](https://risecloud-my.sharepoint.com/personal/anders_thorsen_ri_se/Documents/Microsoft%20Copilot%20Chat%20Files/compute.py)
+from cosmo.app.convert_app import (  # app layer
     ConvertConfig,
     run_convert,
 )
@@ -62,7 +62,7 @@ def _count_topic_messages(mcap_path: Path, topic: str) -> int:
 
 
 @pytest.mark.integration
-@pytest.mark.skipif(not _has_betterosi(), reason="betterosi not installed; cannot write MCAP")  # converter depends on it [1](https://risecloud-my.sharepoint.com/personal/anders_thorsen_ri_se/Documents/Microsoft%20Copilot%20Chat%20Files/openlabel_to_omega.py)
+@pytest.mark.skipif(not _has_betterosi(), reason="betterosi not installed; cannot write MCAP")  # converter depends on it
 @pytest.mark.skipif(not has_mcap_reader(), reason="mcap reader not installed; cannot inspect MCAP")
 def test_mcap_gt_count_map_once_and_strictly_increasing_log_time(tmp_path: Path):
     # Create OpenLABEL with a known number of frames.
@@ -104,7 +104,7 @@ def test_mcap_gt_count_map_once_and_strictly_increasing_log_time(tmp_path: Path)
         encoding="utf-8",
     )
 
-    # OpenDRIVE included so map is embedded as `ground_truth_map` (written once with log_time=0) [1](https://risecloud-my.sharepoint.com/personal/anders_thorsen_ri_se/Documents/Microsoft%20Copilot%20Chat%20Files/openlabel_to_omega.py)
+    # OpenDRIVE included so map is embedded as `ground_truth_map` (written once with log_time=0)
     odr_path = tmp_path / "map.xodr"
     odr_path.write_text("<OpenDRIVE></OpenDRIVE>", encoding="utf-8")
 
@@ -119,10 +119,10 @@ def test_mcap_gt_count_map_once_and_strictly_increasing_log_time(tmp_path: Path)
         write_mcap=True,
         out_dir=str(runs_dir),
         run_name="mcap_gt_count",
-    )  # app layer writes into per-run outputs/ folder [2](https://risecloud-my.sharepoint.com/personal/anders_thorsen_ri_se/Documents/Microsoft%20Copilot%20Chat%20Files/compute.py)
+    )  # app layer writes into per-run outputs/ folder
 
     result = run_convert(cfg, log_fn=None)
-    assert result.mcap_path, "Expected mcap_path to be set when MCAP is written"  # app layer sets only if file exists [2](https://risecloud-my.sharepoint.com/personal/anders_thorsen_ri_se/Documents/Microsoft%20Copilot%20Chat%20Files/compute.py)
+    assert result.mcap_path, "Expected mcap_path to be set when MCAP is written"  # app layer sets only if file exists
 
     mcap_path = assert_mcap_nonempty(result.mcap_path)
 
@@ -130,11 +130,11 @@ def test_mcap_gt_count_map_once_and_strictly_increasing_log_time(tmp_path: Path)
     gt_times = _collect_topic_log_times(mcap_path, "ground_truth")
     assert len(gt_times) == len(frame_ids), f"Expected {len(frame_ids)} ground_truth messages, got {len(gt_times)}"
 
-    # 2) Map message written exactly once at log_time=0 (converter writes once) [1](https://risecloud-my.sharepoint.com/personal/anders_thorsen_ri_se/Documents/Microsoft%20Copilot%20Chat%20Files/openlabel_to_omega.py)
+    # 2) Map message written exactly once at log_time=0 (converter writes once)
     map_times = _collect_topic_log_times(mcap_path, "ground_truth_map")
     assert len(map_times) == 1, f"Expected exactly 1 ground_truth_map message, got {len(map_times)}"
     assert map_times[0] == 0, f"Expected ground_truth_map log_time=0, got {map_times[0]}"
 
-    # 3) GroundTruth log_time strictly increasing (converter uses log_time=total_nanos) [1](https://risecloud-my.sharepoint.com/personal/anders_thorsen_ri_se/Documents/Microsoft%20Copilot%20Chat%20Files/openlabel_to_omega.py)
+    # 3) GroundTruth log_time strictly increasing (converter uses log_time=total_nanos)
     assert gt_times == sorted(gt_times), f"ground_truth log_time not non-decreasing: {gt_times}"
     assert all(b > a for a, b in zip(gt_times, gt_times[1:])), f"ground_truth log_time not strictly increasing: {gt_times}"
diff --git a/tests/test_main_dispatch.py b/tests/test_main_dispatch.py
index c784b48..8dc4554 100644
--- a/tests/test_main_dispatch.py
+++ b/tests/test_main_dispatch.py
@@ -14,5 +14,5 @@ def test_main_version_works_without_gui():
         text=True,
         env={**os.environ, "MPLBACKEND": "Agg"},
     )
-    assert res.returncode == 0  # main.py returns 0 on --version [1](https://risecloud-my.sharepoint.com/personal/anders_thorsen_ri_se/Documents/Microsoft%20Copilot%20Chat%20Files/main.py)
-    assert res.stdout.strip()  # prints version string [1](https://risecloud-my.sharepoint.com/personal/anders_thorsen_ri_se/Documents/Microsoft%20Copilot%20Chat%20Files/main.py)
+    assert res.returncode == 0  # main.py returns 0 on --version
+    assert res.stdout.strip()  # prints version string
diff --git a/tests/test_openlabel_to_omega_whitebox.py b/tests/test_openlabel_to_omega_whitebox.py
index 22f267f..1fedbd5 100644
--- a/tests/test_openlabel_to_omega_whitebox.py
+++ b/tests/test_openlabel_to_omega_whitebox.py
@@ -6,7 +6,7 @@
 
 import numpy as np
 
-from cosmo.converters.openlabel_to_omega import (  # [2](https://risecloud-my.sharepoint.com/personal/anders_thorsen_ri_se/Documents/Microsoft%20Copilot%20Chat%20Files/openlabel_to_omega.py)
+from cosmo.converters.openlabel_to_omega import (  #
     convert_openlabel_to_omega,
     load_alignment,
     parse_openlabel,
@@ -82,7 +82,7 @@ def test_convert_openlabel_to_omega_writes_csv_only(tmp_path: Path):
         georef_data_path=None,
         fps_arg=None,
         write_csv=True,
-        write_mcap=False,  # ensure no betterosi dependency [2](https://risecloud-my.sharepoint.com/personal/anders_thorsen_ri_se/Documents/Microsoft%20Copilot%20Chat%20Files/openlabel_to_omega.py)
+        write_mcap=False,  # ensure no betterosi dependency
         swap_xy=False,
         flip_x=False,
         flip_y=False,
@@ -96,11 +96,11 @@ def test_convert_openlabel_to_omega_writes_csv_only(tmp_path: Path):
 
     with csv_path.open(newline="", encoding="utf-8") as f:
         reader = csv.DictReader(f)
-        # Columns defined in module [2](https://risecloud-my.sharepoint.com/personal/anders_thorsen_ri_se/Documents/Microsoft%20Copilot%20Chat%20Files/openlabel_to_omega.py)
+        # Columns defined in module
         for col in ("total_nanos", "idx", "x", "y", "yaw", "type_name", "subtype_name", "role_name"):
             assert col in (reader.fieldnames or [])
         rows = list(reader)
         assert len(rows) >= 2
-        # Ensure time is non-decreasing (rows are sorted by total_nanos) [2](https://risecloud-my.sharepoint.com/personal/anders_thorsen_ri_se/Documents/Microsoft%20Copilot%20Chat%20Files/openlabel_to_omega.py)
+        # Ensure time is non-decreasing (rows are sorted by total_nanos)
         times = [int(r["total_nanos"]) for r in rows]
         assert times == sorted(times)

From 64676838659a34e759897cf24454394d435f237a Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Anders=20Thors=C3=A9n?=
 <10030664+MickOls@users.noreply.github.com>
Date: Wed, 24 Jun 2026 15:20:25 +0200
Subject: [PATCH 2/2] Remove remaining internal references and patch artifacts

---
 .github/workflows/ci.yml                   |   4 +-
 README.md                                  |   2 +-
 cosmo_required_fixes.patch                 | 533 ---------------------
 cosmo_required_fixes.patch:Zone.Identifier | Bin 25 -> 0 bytes
 docs/how-to/calibration.md                 |   4 +-
 docs/reference/inputs-openlabel.md         |   2 +-
 docs/reference/outputs-omega-prime.md      |   2 +-
 docs/user_guide/cli.md                     |   6 +-
 tests/conftest.py                          |   2 +-
 tests/test_calibrate_cli_validation.py     |   2 +-
 tests/test_cli_contracts_not_smoke.py      |   4 +-
 tests/test_cli_smoke_calibrate.py          |   6 +-
 tests/test_cli_smoke_convert.py            |   4 +-
 tests/test_convert_alignment_flags.py      |   2 +-
 tests/test_convert_cli_validation.py       |   2 +-
 tests/test_convert_outputs.py              |   2 +-
 16 files changed, 22 insertions(+), 555 deletions(-)
 delete mode 100644 cosmo_required_fixes.patch
 delete mode 100644 cosmo_required_fixes.patch:Zone.Identifier

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index 831b249..592c0f3 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -36,7 +36,7 @@ jobs:
         run: ruff check .
 
       # Optional but recommended: verifies console scripts + dispatch without launching GUI.
-      # NOTE: calling plain `cosmo` (no args) attempts to start the GUI by default. [2](https://risecloud-my.sharepoint.com/personal/anders_thorsen_ri_se/Documents/Microsoft%20Copilot%20Chat%20Files/main.py)
+      # NOTE: calling plain `cosmo` (no args) attempts to start the GUI by default.
       - name: CLI sanity check (no GUI)
         run: |
           cosmo --version
@@ -78,4 +78,4 @@ jobs:
       - name: Run integration tests
         env:
           MPLBACKEND: Agg
-        run: pytest -q -m integration
\ No newline at end of file
+        run: pytest -q -m integration
diff --git a/README.md b/README.md
index 91b1d4b..4513c13 100644
--- a/README.md
+++ b/README.md
@@ -81,7 +81,7 @@ Calibration outputs are written to outputs/ as:
 - <base_name>_calibration.json
 - <base_name>_homography_fit_summary.json
 - <base_name>_homography_fit_residuals.png
-- <base_name>_overlay_markers_on_image.png (only if --image is provided) 
+- <base_name>_overlay_markers_on_image.png (only if --image is provided)
 
 Use the calibration file for conversion fallback:
 
diff --git a/cosmo_required_fixes.patch b/cosmo_required_fixes.patch
deleted file mode 100644
index d118fa4..0000000
--- a/cosmo_required_fixes.patch
+++ /dev/null
@@ -1,533 +0,0 @@
---- a/.github/workflows/ci.yml
-+++ b/.github/workflows/ci.yml
-@@ -3,6 +3,10 @@
- on:
-   push:
-   pull_request:
-+  workflow_dispatch:
-+  schedule:
-+    # Run optional/heavier integration tests weekly and on demand.
-+    - cron: "0 3 * * 1"
- 
- jobs:
-   test:
---- a/README.md
-+++ b/README.md
-@@ -52,8 +52,8 @@
- > tools explicitly: `pip install -e . pytest ruff` (adding `betterosi mcap` for
- > MCAP integration tests).
- 
--> Tip 1: The **GUI** is launced with `cosmo` or `cosmo gui`.
--> Tip 2: During development with downloaded repro, all `cosmo` commands can be replaced with `python run_cosmo.py ...`, `cosmo.cmd ...` or `cosmo.ps1 ...`. `python run_gui.py` always starts the **GUI**.
-+> Tip 1: The **GUI** is launched with `cosmo` or `cosmo gui`.
-+> Tip 2: In headless environments, prefer explicit subcommands such as `cosmo convert ...` rather than plain `cosmo`, which may start the GUI.
- 
- Convert using [ORBIT](https://github.com/RI-SE/ORBIT) georef as the primary pixel→ground mapping (**Convert** tab in the **GUI**):
- 
---- a/docs/getting-started/quickstart.md
-+++ b/docs/getting-started/quickstart.md
-@@ -10,17 +10,16 @@
- cosmo gui
- ```
- 
--Development shortcut (either of):
-+Use the installed console script:
- 
- ```bash
--python run_gui.py # Start GUI
--python run_cosmo.py gui # Same behaviour as cosmo (when installed)
--cosmo.cmd gui # Same behaviour in Windows cmd termial as cosmo (when installed)
--cosmo.ps1 gui # Same behaviour in Windows PowerShell termial as cosmo (when installed)
-+cosmo gui
-+# or simply:
-+cosmo
- ```
- ---
- ## CLI
--> During development `cosmo ...` can be replaced with `python run_cosmo ...`, `cosmo.exe ...` or `cosmo.ps1 ...` without needing to install cosmo, e.g., `python run_cosmo.py convert ...`. To install for development use `uv sync --group dev` or `pip install -e . --group dev`.
-+> For development, install the package first (for example `uv sync --group dev` or `pip install -e . --group dev`) and then use the `cosmo ...` console script.
- ---
- ### Convert (recommended: ORBIT georef)
- 
---- a/src/cosmo/converters/openlabel_to_omega.py
-+++ b/src/cosmo/converters/openlabel_to_omega.py
-@@ -721,7 +721,7 @@
-     # ----------------------------
-     # IMPORTANT:
-     # Use betterosi.Writer as a context manager to ensure MCAP footer/summary are finalized properly. [1](https://deepwiki.com/ika-rwth-aachen/omega-prime/3.1-loading-and-saving-recordings)[4](https://ika-rwth-aachen.github.io/omega-prime/notebooks/tutorial/)
--    # Also write topic names without leading "/" to match common omega-prime usage. [3](https://risecloud-my.sharepoint.com/personal/anders_thorsen_ri_se/Documents/Microsoft%20Copilot%20Chat%20Files/convert_app.py)[2](https://risecloud-my.sharepoint.com/personal/anders_thorsen_ri_se/Documents/Microsoft%20Copilot%20Chat%20Files/openlabel_to_omega.py)
-+    # Also write topic names without leading "/" to match common omega-prime usage.
- 
-     def _write_map(writer_mcap):
-         if odr_path and os.path.isfile(odr_path):
-@@ -752,7 +752,7 @@
-             gt.proj_string = _gt_proj_string
-         if _gt_country_code:
-             gt.country_code = _gt_country_code
--        # Provide log_time explicitly; readers often build indices from it. [4](https://ika-rwth-aachen.github.io/omega-prime/notebooks/tutorial/)[3](https://risecloud-my.sharepoint.com/personal/anders_thorsen_ri_se/Documents/Microsoft%20Copilot%20Chat%20Files/convert_app.py)
-+        # Provide log_time explicitly; readers often build indices from it. [4](https://ika-rwth-aachen.github.io/omega-prime/notebooks/tutorial/)
-         writer_mcap.add(gt, topic="ground_truth", log_time=total_nanos)
- 
-     # If MCAP enabled, write with context manager; else only build CSV rows
---- a/src/cosmo/gui/main_window.py
-+++ b/src/cosmo/gui/main_window.py
-@@ -9,7 +9,7 @@
- from pathlib import Path
- from typing import Optional
- 
--# Qt binding selection: PyQt5 → PySide6 → PyQt6 (same as your current GUI). [1](https://risecloud-my.sharepoint.com/personal/anders_thorsen_ri_se/Documents/Microsoft%20Copilot%20Chat%20Files/convert_openlabel_to_omega.py)
-+# Qt binding selection: PyQt5 → PySide6 → PyQt6 (same as your current GUI).
- try:
-     from PyQt5 import QtCore, QtGui, QtWidgets
-     _QT_API = "PyQt5"
---- a/src/cosmo/gui/workers.py
-+++ b/src/cosmo/gui/workers.py
-@@ -3,7 +3,7 @@
- 
- from typing import Callable
- 
--# Qt binding selection (same preference order as your current GUI) [1](https://risecloud-my.sharepoint.com/personal/anders_thorsen_ri_se/Documents/Microsoft%20Copilot%20Chat%20Files/convert_openlabel_to_omega.py)
-+# Qt binding selection (same preference order as your current GUI)
- try:
-     from PyQt5 import QtCore
-     _Signal = QtCore.pyqtSignal
---- a/tests/cli_helpers.py
-+++ b/tests/cli_helpers.py
-@@ -21,10 +21,10 @@
-     env.setdefault("MPLBACKEND", "Agg")
- 
-     if os.name == "nt":
--        cmd = [sys.executable, "-m", "cosmo.cli.main", *args]  # real entrypoint logic [3](https://risecloud-my.sharepoint.com/personal/anders_thorsen_ri_se/Documents/Microsoft%20Copilot%20Chat%20Files/main.py)
-+        cmd = [sys.executable, "-m", "cosmo.cli.main", *args]  # real entrypoint logic
-     else:
-         exe = shutil.which("cosmo")
--        cmd = [exe, *args] if exe else [sys.executable, "-m", "cosmo.cli.main", *args]  # same entrypoint [3](https://risecloud-my.sharepoint.com/personal/anders_thorsen_ri_se/Documents/Microsoft%20Copilot%20Chat%20Files/main.py)
-+        cmd = [exe, *args] if exe else [sys.executable, "-m", "cosmo.cli.main", *args]  # same entrypoint
- 
-     return subprocess.run(cmd, cwd=str(cwd), capture_output=True, text=True, env=env)
- 
---- a/tests/conftest.py
-+++ b/tests/conftest.py
-@@ -16,7 +16,7 @@
-     Fallback: if the console script isn't on PATH (rare in CI), run via module entrypoint:
-         python -m cosmo.cli.main <args...>
- 
--    NOTE: Never call plain `cosmo` with no args in CI, because cosmo.cli.main defaults to GUI. [2](https://risecloud-my.sharepoint.com/personal/anders_thorsen_ri_se/Documents/Microsoft%20Copilot%20Chat%20Files/main.py)
-+    NOTE: Never call plain `cosmo` with no args in CI, because cosmo.cli.main defaults to GUI.
-     """
-     env = dict(os.environ)
-     env.setdefault("MPLBACKEND", "Agg")  # CI already sets this, but keep it deterministic. [1](blob:https://www.microsoft365.com/3377b2c7-ce90-4a5f-bcf4-96fccf281101)
-@@ -26,7 +26,7 @@
-         cmd = [exe, *args]
-     else:
-         # Still the real entrypoint, just executed as a module.
--        cmd = [os.environ.get("PYTHON", "python"), "-m", "cosmo.cli.main", *args]  # dispatch logic in main.py [2](https://risecloud-my.sharepoint.com/personal/anders_thorsen_ri_se/Documents/Microsoft%20Copilot%20Chat%20Files/main.py)
-+        cmd = [os.environ.get("PYTHON", "python"), "-m", "cosmo.cli.main", *args]  # dispatch logic in main.py
- 
-     return subprocess.run(cmd, cwd=str(cwd), capture_output=True, text=True, env=env)
- 
---- a/tests/test_calibration_compute_whitebox.py
-+++ b/tests/test_calibration_compute_whitebox.py
-@@ -6,7 +6,7 @@
- import numpy as np
- import pytest
- 
--from cosmo.calibration.compute import (  # [1](https://risecloud-my.sharepoint.com/personal/anders_thorsen_ri_se/Documents/Microsoft%20Copilot%20Chat%20Files/compute.py)
-+from cosmo.calibration.compute import (  #
-     compute_calibration,
-     write_calibration_outputs,
- )
-@@ -75,7 +75,7 @@
-         fps=30.0,
-         image_width=3840,
-         image_height=2160,
--        residuals_png_path=str(resid_png),  # optional; may become None on plot errors [1](https://risecloud-my.sharepoint.com/personal/anders_thorsen_ri_se/Documents/Microsoft%20Copilot%20Chat%20Files/compute.py)
-+        residuals_png_path=str(resid_png),  # optional; may become None on plot errors
-         overlay_png_path=None,
-         image_path=None,
-         openlabel_path=None,
-@@ -85,7 +85,7 @@
-     assert Path(outs.summary_json_path).is_file()
- 
-     calib = json.loads(Path(outs.calibration_json_path).read_text(encoding="utf-8"))
--    # Required keys written by write_calibration_outputs [1](https://risecloud-my.sharepoint.com/personal/anders_thorsen_ri_se/Documents/Microsoft%20Copilot%20Chat%20Files/compute.py)
-+    # Required keys written by write_calibration_outputs
-     for k in ("fps", "image_width", "image_height", "homography", "intrinsics", "extrinsics", "default_dimensions_m"):
-         assert k in calib
-     H = calib["homography"]
-@@ -95,7 +95,7 @@
-     for k in ("rmse_m", "inliers_count", "pairs_used", "pixel_points", "world_points_ENU_m", "homography"):
-         assert k in summary
- 
--    # Residual plot can be omitted if matplotlib errors; if present, ensure file exists [1](https://risecloud-my.sharepoint.com/personal/anders_thorsen_ri_se/Documents/Microsoft%20Copilot%20Chat%20Files/compute.py)
-+    # Residual plot can be omitted if matplotlib errors; if present, ensure file exists
-     if outs.residuals_png_path is not None:
-         assert Path(outs.residuals_png_path).is_file()
- 
---- a/tests/test_console_scripts_smoke.py
-+++ b/tests/test_console_scripts_smoke.py
-@@ -50,19 +50,19 @@
-     assert cosmo_calibrate, "Expected 'cosmo-calibrate' on PATH or in venv bin dir after install."
-     assert cosmo_gui, "Expected 'cosmo-gui' on PATH or in venv bin dir after install."
- 
--    # Always safe: module entrypoint tests real main.py behavior. [3](https://risecloud-my.sharepoint.com/personal/anders_thorsen_ri_se/Documents/Microsoft%20Copilot%20Chat%20Files/main.py)
-+    # Always safe: module entrypoint tests real main.py behavior.
-     res = _run([sys.executable, "-m", "cosmo.cli.main", "--version"])
-     assert res.returncode == 0, f"cosmo --version failed.\nSTDOUT:\n{res.stdout}\nSTDERR:\n{res.stderr}"
-     assert res.stdout.strip(), "cosmo --version produced no output."
- 
--    # Dispatch help via main.py (convert/calibrate are subcommands). [3](https://risecloud-my.sharepoint.com/personal/anders_thorsen_ri_se/Documents/Microsoft%20Copilot%20Chat%20Files/main.py)
-+    # Dispatch help via main.py (convert/calibrate are subcommands).
-     res = _run([sys.executable, "-m", "cosmo.cli.main", "convert", "--help"])
-     assert res.returncode == 0, f"cosmo convert --help failed.\nSTDOUT:\n{res.stdout}\nSTDERR:\n{res.stderr}"
- 
-     res = _run([sys.executable, "-m", "cosmo.cli.main", "calibrate", "--help"])
-     assert res.returncode == 0, f"cosmo calibrate --help failed.\nSTDOUT:\n{res.stdout}\nSTDERR:\n{res.stderr}"
- 
--    # Direct entrypoints: run via module on Windows to avoid blocked .EXE shims. [1](https://risecloud-my.sharepoint.com/personal/anders_thorsen_ri_se/Documents/Microsoft%20Copilot%20Chat%20Files/main.py)[2](https://risecloud-my.sharepoint.com/personal/anders_thorsen_ri_se/Documents/Microsoft%20Copilot%20Chat%20Files/main.py)
-+    # Direct entrypoints: run via module on Windows to avoid blocked .EXE shims.
-     if os.name == "nt":
-         res = _run([sys.executable, "-m", "cosmo.cli.convert", "--help"])
-         assert res.returncode == 0, f"python -m cosmo.cli.convert --help failed.\nSTDOUT:\n{res.stdout}\nSTDERR:\n{res.stderr}"
-@@ -76,4 +76,4 @@
-         res = _run([cosmo_calibrate, "--help"])
-         assert res.returncode == 0, f"cosmo-calibrate --help failed.\nSTDOUT:\n{res.stdout}\nSTDERR:\n{res.stderr}"
- 
--    # Do NOT execute cosmo-gui in tests: it launches GUI immediately and can fail headless. [3](https://risecloud-my.sharepoint.com/personal/anders_thorsen_ri_se/Documents/Microsoft%20Copilot%20Chat%20Files/main.py)[3](https://risecloud-my.sharepoint.com/personal/anders_thorsen_ri_se/Documents/Microsoft%20Copilot%20Chat%20Files/main.py)
-+    # Do NOT execute cosmo-gui in tests: it launches GUI immediately and can fail headless.
---- a/tests/test_convert_app_e2e_not_smoke.py
-+++ b/tests/test_convert_app_e2e_not_smoke.py
-@@ -5,7 +5,7 @@
- import json
- from pathlib import Path
- 
--from cosmo.app.convert_app import (  # [1](https://risecloud-my.sharepoint.com/personal/anders_thorsen_ri_se/Documents/Microsoft%20Copilot%20Chat%20Files/compute.py)
-+from cosmo.app.convert_app import (  #
-     ConvertConfig,
-     run_convert,
- )
---- a/tests/test_convert_no_scripts_fallback.py
-+++ b/tests/test_convert_no_scripts_fallback.py
-@@ -2,7 +2,7 @@
- from __future__ import annotations
- 
- from cosmo.app.convert_app import (
--    _get_converter_or_raise,  # internal helper [2](https://risecloud-my.sharepoint.com/personal/anders_thorsen_ri_se/Documents/Microsoft%20Copilot%20Chat%20Files/convert_app.py)
-+    _get_converter_or_raise,  # internal helper
- )
- 
- 
-@@ -11,7 +11,7 @@
-         fn = _get_converter_or_raise()
-         assert callable(fn)
-     except RuntimeError as e:
--        # If it fails, ensure the error message guides the developer correctly. [2](https://risecloud-my.sharepoint.com/personal/anders_thorsen_ri_se/Documents/Microsoft%20Copilot%20Chat%20Files/convert_app.py)
-+        # If it fails, ensure the error message guides the developer correctly.
-         msg = str(e)
-         assert "COSMO converter implementation not found" in msg
-         assert "cosmo.converters.openlabel_to_omega" in msg
---- a/tests/test_core_calibrate_whitebox.py
-+++ b/tests/test_core_calibrate_whitebox.py
-@@ -3,7 +3,7 @@
- import json
- from pathlib import Path
- 
--from cosmo.app.calibrate_app import (  # app layer API [1](https://risecloud-my.sharepoint.com/personal/anders_thorsen_ri_se/Documents/Microsoft%20Copilot%20Chat%20Files/calibrate_app.py)
-+from cosmo.app.calibrate_app import (  # app layer API
-     CalibrateConfig,
-     run_calibrate,
- )
-@@ -34,7 +34,7 @@
-     opendrive = tmp_path / "map.xodr"
-     opendrive.write_text("<OpenDRIVE></OpenDRIVE>", encoding="utf-8")
- 
--    # Deterministic run folder: existing out_dir + run_name => out_dir/run_name [1](https://risecloud-my.sharepoint.com/personal/anders_thorsen_ri_se/Documents/Microsoft%20Copilot%20Chat%20Files/calibrate_app.py)
-+    # Deterministic run folder: existing out_dir + run_name => out_dir/run_name
-     runs_dir = tmp_path / "runs"
-     runs_dir.mkdir()
- 
-@@ -55,7 +55,7 @@
-     )
- 
-     logs: list[str] = []
--    result = run_calibrate(cfg, log_fn=logs.append)  # same signature used by CLI [1](https://risecloud-my.sharepoint.com/personal/anders_thorsen_ri_se/Documents/Microsoft%20Copilot%20Chat%20Files/calibrate_app.py)
-+    result = run_calibrate(cfg, log_fn=logs.append)  # same signature used by CLI
- 
-     run_dir = Path(result.run_dir)
-     outputs_dir = Path(result.outputs_dir)
-@@ -63,7 +63,7 @@
-     assert outputs_dir == run_dir / "outputs"
-     assert outputs_dir.exists()
- 
--    # Output naming is stem-based: <base>_calibration.json etc. [1](https://risecloud-my.sharepoint.com/personal/anders_thorsen_ri_se/Documents/Microsoft%20Copilot%20Chat%20Files/calibrate_app.py)
-+    # Output naming is stem-based: <base>_calibration.json etc.
-     calib_path = Path(result.calibration_json_path)
-     assert calib_path.is_file()
-     assert calib_path.name.endswith("_calibration.json")
-@@ -73,15 +73,15 @@
-     H = calib["homography"]
-     assert isinstance(H, list) and len(H) == 3 and all(len(r) == 3 for r in H)
- 
--    # Summary JSON should be produced (unless compute/write changes) [1](https://risecloud-my.sharepoint.com/personal/anders_thorsen_ri_se/Documents/Microsoft%20Copilot%20Chat%20Files/calibrate_app.py)
-+    # Summary JSON should be produced (unless compute/write changes)
-     if result.summary_json_path:
-         assert Path(result.summary_json_path).is_file()
- 
--    # Residual plot is intended but can be None (matplotlib issues), so keep optional. [1](https://risecloud-my.sharepoint.com/personal/anders_thorsen_ri_se/Documents/Microsoft%20Copilot%20Chat%20Files/calibrate_app.py)
-+    # Residual plot is intended but can be None (matplotlib issues), so keep optional.
-     if result.residuals_png_path:
-         assert Path(result.residuals_png_path).is_file()
- 
--    # No overlay expected because image=None [1](https://risecloud-my.sharepoint.com/personal/anders_thorsen_ri_se/Documents/Microsoft%20Copilot%20Chat%20Files/calibrate_app.py)
-+    # No overlay expected because image=None
-     assert result.overlay_png_path is None
- 
-     # Some logging should occur (useful diagnostic)
---- a/tests/test_core_convert_whitebox.py
-+++ b/tests/test_core_convert_whitebox.py
-@@ -4,7 +4,7 @@
- import json
- from pathlib import Path
- 
--from cosmo.app.convert_app import (  # app layer API [2](https://risecloud-my.sharepoint.com/personal/anders_thorsen_ri_se/Documents/Microsoft%20Copilot%20Chat%20Files/convert_app.py)
-+from cosmo.app.convert_app import (  # app layer API
-     ConvertConfig,
-     run_convert,
- )
-@@ -31,7 +31,7 @@
-     openlabel_path = tmp_path / "openlabel.json"
-     openlabel_path.write_text(json.dumps(openlabel), encoding="utf-8")
- 
--    # Minimal calibration file path (convert_app passes this to converter if provided) [2](https://risecloud-my.sharepoint.com/personal/anders_thorsen_ri_se/Documents/Microsoft%20Copilot%20Chat%20Files/convert_app.py)
-+    # Minimal calibration file path (convert_app passes this to converter if provided)
-     calib = {
-         "fps": 30.0,
-         "image_width": 3840,
-@@ -51,7 +51,7 @@
-         calibration=str(calib_path),
-         fps=None,
-         write_csv=True,
--        write_mcap=False,  # keep core tests independent of optional MCAP deps [2](https://risecloud-my.sharepoint.com/personal/anders_thorsen_ri_se/Documents/Microsoft%20Copilot%20Chat%20Files/convert_app.py)
-+        write_mcap=False,  # keep core tests independent of optional MCAP deps
-         swap_xy=False,
-         flip_x=False,
-         flip_y=False,
-@@ -62,7 +62,7 @@
-     )
- 
-     logs: list[str] = []
--    result = run_convert(cfg, log_fn=logs.append)  # same signature used by CLI [2](https://risecloud-my.sharepoint.com/personal/anders_thorsen_ri_se/Documents/Microsoft%20Copilot%20Chat%20Files/convert_app.py)
-+    result = run_convert(cfg, log_fn=logs.append)  # same signature used by CLI
- 
-     run_dir = Path(result.run_dir)
-     outputs_dir = Path(result.outputs_dir)
-@@ -70,7 +70,7 @@
-     assert outputs_dir == run_dir / "outputs"
-     assert outputs_dir.exists()
- 
--    # csv_path is only set if the file exists (summary filters non-existent files) [2](https://risecloud-my.sharepoint.com/personal/anders_thorsen_ri_se/Documents/Microsoft%20Copilot%20Chat%20Files/convert_app.py)
-+    # csv_path is only set if the file exists (summary filters non-existent files)
-     assert result.csv_path is not None
-     csv_path = Path(result.csv_path)
-     assert csv_path.is_file()
-@@ -103,7 +103,7 @@
-         write_mcap=False,
-         out_dir=str(runs_dir),
-         run_name="wb_no_csv",
--    )  # relies on defaults for other fields [2](https://risecloud-my.sharepoint.com/personal/anders_thorsen_ri_se/Documents/Microsoft%20Copilot%20Chat%20Files/convert_app.py)
-+    )  # relies on defaults for other fields
- 
-     result = run_convert(cfg, log_fn=lambda _: None)
-     assert result.csv_path is None
---- a/tests/test_integration_mcap_convert_app.py
-+++ b/tests/test_integration_mcap_convert_app.py
-@@ -5,7 +5,7 @@
- 
- import pytest
- 
--from cosmo.app.convert_app import (  # [3](https://risecloud-my.sharepoint.com/personal/anders_thorsen_ri_se/Documents/Microsoft%20Copilot%20Chat%20Files/compute.py)
-+from cosmo.app.convert_app import (  #
-     ConvertConfig,
-     run_convert,
- )
-@@ -20,7 +20,7 @@
- 
- 
- @pytest.mark.integration
--@pytest.mark.skipif(not _has_betterosi(), reason="betterosi not installed; MCAP integration test skipped")  # [1](https://risecloud-my.sharepoint.com/personal/anders_thorsen_ri_se/Documents/Microsoft%20Copilot%20Chat%20Files/openlabel_to_omega.py)
-+@pytest.mark.skipif(not _has_betterosi(), reason="betterosi not installed; MCAP integration test skipped")  #
- def test_run_convert_app_writes_mcap_and_sets_result_path(tmp_path: Path):
-     # Minimal OpenLABEL
-     openlabel = {
-@@ -36,7 +36,7 @@
-     calib_path = tmp_path / "Calibration.json"
-     calib_path.write_text(json.dumps({"fps": 10.0, "homography": [[1, 0, 0], [0, 1, 0], [0, 0, 1]]}), encoding="utf-8")
- 
--    # OpenDRIVE embedded flag in convert_app summary is based on cfg.opendrive [3](https://risecloud-my.sharepoint.com/personal/anders_thorsen_ri_se/Documents/Microsoft%20Copilot%20Chat%20Files/compute.py)
-+    # OpenDRIVE embedded flag in convert_app summary is based on cfg.opendrive
-     odr_path = tmp_path / "map.xodr"
-     odr_path.write_text("<OpenDRIVE></OpenDRIVE>", encoding="utf-8")
- 
-@@ -51,14 +51,14 @@
-         write_mcap=True,
-         out_dir=str(runs_dir),
-         run_name="int_mcap",
--    )  # config matches app layer [3](https://risecloud-my.sharepoint.com/personal/anders_thorsen_ri_se/Documents/Microsoft%20Copilot%20Chat%20Files/compute.py)
-+    )  # config matches app layer
- 
-     result = run_convert(cfg, log_fn=None)
- 
-     assert Path(result.run_dir).exists()
-     assert Path(result.outputs_dir).exists()
- 
--    # convert_app only sets mcap_path if file exists [3](https://risecloud-my.sharepoint.com/personal/anders_thorsen_ri_se/Documents/Microsoft%20Copilot%20Chat%20Files/compute.py)
-+    # convert_app only sets mcap_path if file exists
-     assert result.mcap_path is not None
-     assert Path(result.mcap_path).is_file()
-     assert Path(result.mcap_path).stat().st_size > 0
---- a/tests/test_integration_mcap_converter.py
-+++ b/tests/test_integration_mcap_converter.py
-@@ -6,7 +6,7 @@
- import pytest
- 
- from cosmo.converters.openlabel_to_omega import (
--    convert_openlabel_to_omega,  # [1](https://risecloud-my.sharepoint.com/personal/anders_thorsen_ri_se/Documents/Microsoft%20Copilot%20Chat%20Files/openlabel_to_omega.py)
-+    convert_openlabel_to_omega,  #
- )
- 
- 
-@@ -37,7 +37,7 @@
- 
- 
- @pytest.mark.integration
--@pytest.mark.skipif(not _has_betterosi(), reason="betterosi not installed; MCAP integration test skipped")  # [1](https://risecloud-my.sharepoint.com/personal/anders_thorsen_ri_se/Documents/Microsoft%20Copilot%20Chat%20Files/openlabel_to_omega.py)
-+@pytest.mark.skipif(not _has_betterosi(), reason="betterosi not installed; MCAP integration test skipped")  #
- def test_converter_writes_mcap_with_ground_truth_and_map(tmp_path: Path):
-     # Minimal OpenLABEL with two frames (ensures multiple GT messages)
-     openlabel = {
-@@ -67,7 +67,7 @@
-         encoding="utf-8",
-     )
- 
--    # Provide OpenDRIVE so map embedding path is exercised (ground_truth_map topic) [1](https://risecloud-my.sharepoint.com/personal/anders_thorsen_ri_se/Documents/Microsoft%20Copilot%20Chat%20Files/openlabel_to_omega.py)
-+    # Provide OpenDRIVE so map embedding path is exercised (ground_truth_map topic)
-     odr_path = tmp_path / "map.xodr"
-     odr_path.write_text("<OpenDRIVE></OpenDRIVE>", encoding="utf-8")
- 
-@@ -82,7 +82,7 @@
-         georef_data_path=None,
-         fps_arg=None,
-         write_csv=False,   # focus on MCAP in this integration test
--        write_mcap=True,   # requires betterosi [1](https://risecloud-my.sharepoint.com/personal/anders_thorsen_ri_se/Documents/Microsoft%20Copilot%20Chat%20Files/openlabel_to_omega.py)
-+        write_mcap=True,   # requires betterosi
-         swap_xy=False,
-         flip_x=False,
-         flip_y=False,
-@@ -98,6 +98,6 @@
-     # Optional deeper validation if the `mcap` reader is installed:
-     topics = _try_read_mcap_topics(mcap_path)
-     if topics:
--        # Converter writes these topics without leading '/' [1](https://risecloud-my.sharepoint.com/personal/anders_thorsen_ri_se/Documents/Microsoft%20Copilot%20Chat%20Files/openlabel_to_omega.py)
-+        # Converter writes these topics without leading '/'
-         assert "ground_truth" in topics
-         assert "ground_truth_map" in topics
---- a/tests/test_integration_mcap_gt_count.py
-+++ b/tests/test_integration_mcap_gt_count.py
-@@ -23,7 +23,7 @@
- 
- import pytest
- 
--from cosmo.app.convert_app import (  # app layer [2](https://risecloud-my.sharepoint.com/personal/anders_thorsen_ri_se/Documents/Microsoft%20Copilot%20Chat%20Files/compute.py)
-+from cosmo.app.convert_app import (  # app layer
-     ConvertConfig,
-     run_convert,
- )
-@@ -62,7 +62,7 @@
- 
- 
- @pytest.mark.integration
--@pytest.mark.skipif(not _has_betterosi(), reason="betterosi not installed; cannot write MCAP")  # converter depends on it [1](https://risecloud-my.sharepoint.com/personal/anders_thorsen_ri_se/Documents/Microsoft%20Copilot%20Chat%20Files/openlabel_to_omega.py)
-+@pytest.mark.skipif(not _has_betterosi(), reason="betterosi not installed; cannot write MCAP")  # converter depends on it
- @pytest.mark.skipif(not has_mcap_reader(), reason="mcap reader not installed; cannot inspect MCAP")
- def test_mcap_gt_count_map_once_and_strictly_increasing_log_time(tmp_path: Path):
-     # Create OpenLABEL with a known number of frames.
-@@ -104,7 +104,7 @@
-         encoding="utf-8",
-     )
- 
--    # OpenDRIVE included so map is embedded as `ground_truth_map` (written once with log_time=0) [1](https://risecloud-my.sharepoint.com/personal/anders_thorsen_ri_se/Documents/Microsoft%20Copilot%20Chat%20Files/openlabel_to_omega.py)
-+    # OpenDRIVE included so map is embedded as `ground_truth_map` (written once with log_time=0)
-     odr_path = tmp_path / "map.xodr"
-     odr_path.write_text("<OpenDRIVE></OpenDRIVE>", encoding="utf-8")
- 
-@@ -119,10 +119,10 @@
-         write_mcap=True,
-         out_dir=str(runs_dir),
-         run_name="mcap_gt_count",
--    )  # app layer writes into per-run outputs/ folder [2](https://risecloud-my.sharepoint.com/personal/anders_thorsen_ri_se/Documents/Microsoft%20Copilot%20Chat%20Files/compute.py)
-+    )  # app layer writes into per-run outputs/ folder
- 
-     result = run_convert(cfg, log_fn=None)
--    assert result.mcap_path, "Expected mcap_path to be set when MCAP is written"  # app layer sets only if file exists [2](https://risecloud-my.sharepoint.com/personal/anders_thorsen_ri_se/Documents/Microsoft%20Copilot%20Chat%20Files/compute.py)
-+    assert result.mcap_path, "Expected mcap_path to be set when MCAP is written"  # app layer sets only if file exists
- 
-     mcap_path = assert_mcap_nonempty(result.mcap_path)
- 
-@@ -130,11 +130,11 @@
-     gt_times = _collect_topic_log_times(mcap_path, "ground_truth")
-     assert len(gt_times) == len(frame_ids), f"Expected {len(frame_ids)} ground_truth messages, got {len(gt_times)}"
- 
--    # 2) Map message written exactly once at log_time=0 (converter writes once) [1](https://risecloud-my.sharepoint.com/personal/anders_thorsen_ri_se/Documents/Microsoft%20Copilot%20Chat%20Files/openlabel_to_omega.py)
-+    # 2) Map message written exactly once at log_time=0 (converter writes once)
-     map_times = _collect_topic_log_times(mcap_path, "ground_truth_map")
-     assert len(map_times) == 1, f"Expected exactly 1 ground_truth_map message, got {len(map_times)}"
-     assert map_times[0] == 0, f"Expected ground_truth_map log_time=0, got {map_times[0]}"
- 
--    # 3) GroundTruth log_time strictly increasing (converter uses log_time=total_nanos) [1](https://risecloud-my.sharepoint.com/personal/anders_thorsen_ri_se/Documents/Microsoft%20Copilot%20Chat%20Files/openlabel_to_omega.py)
-+    # 3) GroundTruth log_time strictly increasing (converter uses log_time=total_nanos)
-     assert gt_times == sorted(gt_times), f"ground_truth log_time not non-decreasing: {gt_times}"
-     assert all(b > a for a, b in zip(gt_times, gt_times[1:])), f"ground_truth log_time not strictly increasing: {gt_times}"
---- a/tests/test_main_dispatch.py
-+++ b/tests/test_main_dispatch.py
-@@ -14,5 +14,5 @@
-         text=True,
-         env={**os.environ, "MPLBACKEND": "Agg"},
-     )
--    assert res.returncode == 0  # main.py returns 0 on --version [1](https://risecloud-my.sharepoint.com/personal/anders_thorsen_ri_se/Documents/Microsoft%20Copilot%20Chat%20Files/main.py)
--    assert res.stdout.strip()  # prints version string [1](https://risecloud-my.sharepoint.com/personal/anders_thorsen_ri_se/Documents/Microsoft%20Copilot%20Chat%20Files/main.py)
-+    assert res.returncode == 0  # main.py returns 0 on --version
-+    assert res.stdout.strip()  # prints version string
---- a/tests/test_openlabel_to_omega_whitebox.py
-+++ b/tests/test_openlabel_to_omega_whitebox.py
-@@ -6,7 +6,7 @@
- 
- import numpy as np
- 
--from cosmo.converters.openlabel_to_omega import (  # [2](https://risecloud-my.sharepoint.com/personal/anders_thorsen_ri_se/Documents/Microsoft%20Copilot%20Chat%20Files/openlabel_to_omega.py)
-+from cosmo.converters.openlabel_to_omega import (  #
-     convert_openlabel_to_omega,
-     load_alignment,
-     parse_openlabel,
-@@ -82,7 +82,7 @@
-         georef_data_path=None,
-         fps_arg=None,
-         write_csv=True,
--        write_mcap=False,  # ensure no betterosi dependency [2](https://risecloud-my.sharepoint.com/personal/anders_thorsen_ri_se/Documents/Microsoft%20Copilot%20Chat%20Files/openlabel_to_omega.py)
-+        write_mcap=False,  # ensure no betterosi dependency
-         swap_xy=False,
-         flip_x=False,
-         flip_y=False,
-@@ -96,11 +96,11 @@
- 
-     with csv_path.open(newline="", encoding="utf-8") as f:
-         reader = csv.DictReader(f)
--        # Columns defined in module [2](https://risecloud-my.sharepoint.com/personal/anders_thorsen_ri_se/Documents/Microsoft%20Copilot%20Chat%20Files/openlabel_to_omega.py)
-+        # Columns defined in module
-         for col in ("total_nanos", "idx", "x", "y", "yaw", "type_name", "subtype_name", "role_name"):
-             assert col in (reader.fieldnames or [])
-         rows = list(reader)
-         assert len(rows) >= 2
--        # Ensure time is non-decreasing (rows are sorted by total_nanos) [2](https://risecloud-my.sharepoint.com/personal/anders_thorsen_ri_se/Documents/Microsoft%20Copilot%20Chat%20Files/openlabel_to_omega.py)
-+        # Ensure time is non-decreasing (rows are sorted by total_nanos)
-         times = [int(r["total_nanos"]) for r in rows]
-         assert times == sorted(times)
diff --git a/cosmo_required_fixes.patch:Zone.Identifier b/cosmo_required_fixes.patch:Zone.Identifier
deleted file mode 100644
index d6c1ec682968c796b9f5e9e080cc6f674b57c766..0000000000000000000000000000000000000000
GIT binary patch
literal 0
HcmV?d00001

literal 25
dcma!!%Fjy;DN4*MPD?F{<>dl#JyUFr831@K2x<TT

diff --git a/docs/how-to/calibration.md b/docs/how-to/calibration.md
index 035403f..2eb7ba8 100644
--- a/docs/how-to/calibration.md
+++ b/docs/how-to/calibration.md
@@ -17,7 +17,7 @@ The calibration JSON is written as:
 Other helpful artifacts:
 - <base_name>_homography_fit_summary.json
 - <base_name>_homography_fit_residuals.png
-- <base_name>_overlay_markers_on_image.png (only if --image was supplied) 
+- <base_name>_overlay_markers_on_image.png (only if --image was supplied)
 
 ## Step 3 — Convert using calibration
 
@@ -31,4 +31,4 @@ cosmo convert scenario.json \
 If results look wrong, check the calibration run’s run_summary.json for:
 
 - RMSE and inlier count
-- notes about missing plots/overlays 
+- notes about missing plots/overlays
diff --git a/docs/reference/inputs-openlabel.md b/docs/reference/inputs-openlabel.md
index ac7e38f..e776e92 100644
--- a/docs/reference/inputs-openlabel.md
+++ b/docs/reference/inputs-openlabel.md
@@ -1,6 +1,6 @@
 # Input: OpenLABEL (expected structure)
 
-COSMO reads OpenLABEL JSON and extracts object metadata and per-frame rotated bounding boxes (rbbox). 
+COSMO reads OpenLABEL JSON and extracts object metadata and per-frame rotated bounding boxes (rbbox).
 
 ## Required content
 COSMO expects, per frame, objects that contain an `rbbox` with at least five values:
diff --git a/docs/reference/outputs-omega-prime.md b/docs/reference/outputs-omega-prime.md
index f4fefdb..a83041a 100644
--- a/docs/reference/outputs-omega-prime.md
+++ b/docs/reference/outputs-omega-prime.md
@@ -1,6 +1,6 @@
 # Outputs: Omega‑Prime CSV + OSI/MCAP
 
-COSMO writes all outputs inside a per-run folder under `runs/` by default. 
+COSMO writes all outputs inside a per-run folder under `runs/` by default.
 
 ---
 
diff --git a/docs/user_guide/cli.md b/docs/user_guide/cli.md
index 890e2f1..22e6a9d 100644
--- a/docs/user_guide/cli.md
+++ b/docs/user_guide/cli.md
@@ -61,7 +61,7 @@ cosmo convert scenario.json \
   --xy-offset 1.2 -0.5 \
   -o runs/
 ```
-Available flags: `--swap-xy`, `--flip-x`, `--flip-y`, `--xy-offset DX DY`, `--yaw-offset-deg DEG`. 
+Available flags: `--swap-xy`, `--flip-x`, `--flip-y`, `--xy-offset DX DY`, `--yaw-offset-deg DEG`.
 ### Run naming & JSON output
 ```bash
 cosmo convert scenario.json --run-name saro_roundabout -o runs/
@@ -144,7 +144,7 @@ cosmo calibrate --inputs pixel_pairs.csv visual_markers.csv map.xodr \
 
 ##### Useful knobs
 - --ransac-thresh-m (default 0.50) — RANSAC distance threshold in meters --fps,
-- --image-width, --image-height 
+- --image-width, --image-height
 
 ##### Calibration outputs
 Calibration writes stem-based files under outputs/:
@@ -152,5 +152,5 @@ Calibration writes stem-based files under outputs/:
 - <base_name>_calibration.json
 - <base_name>_homography_fit_summary.json
 - <base_name>_homography_fit_residuals.png
-- <base_name>_overlay_markers_on_image.png (only if --image is provided) 
+- <base_name>_overlay_markers_on_image.png (only if --image is provided)
 
diff --git a/tests/conftest.py b/tests/conftest.py
index 4f94ab9..3f80e69 100644
--- a/tests/conftest.py
+++ b/tests/conftest.py
@@ -19,7 +19,7 @@ def run_cosmo(args: list[str], *, cwd: Path) -> subprocess.CompletedProcess[str]
     NOTE: Never call plain `cosmo` with no args in CI, because cosmo.cli.main defaults to GUI.
     """
     env = dict(os.environ)
-    env.setdefault("MPLBACKEND", "Agg")  # CI already sets this, but keep it deterministic. [1](blob:https://www.microsoft365.com/3377b2c7-ce90-4a5f-bcf4-96fccf281101)
+    env.setdefault("MPLBACKEND", "Agg")  # CI already sets this, but keep it deterministic.
 
     exe = shutil.which("cosmo")
     if exe:
diff --git a/tests/test_calibrate_cli_validation.py b/tests/test_calibrate_cli_validation.py
index 0740b11..9eefbb6 100644
--- a/tests/test_calibrate_cli_validation.py
+++ b/tests/test_calibrate_cli_validation.py
@@ -20,4 +20,4 @@ def test_calibrate_rejects_mixed_input_styles(tmp_path: Path):
         cwd=tmp_path,
     )
     assert res.returncode != 0
-    assert "Mixed input styles detected" in (res.stderr + res.stdout)  # error text comes from argparse error [2](blob:https://www.microsoft365.com/c655cd7d-9ac4-4928-84e7-b9a8f04405bd)
+    assert "Mixed input styles detected" in (res.stderr + res.stdout)  # error text comes from argparse error
diff --git a/tests/test_cli_contracts_not_smoke.py b/tests/test_cli_contracts_not_smoke.py
index 6df2b00..1c25858 100644
--- a/tests/test_cli_contracts_not_smoke.py
+++ b/tests/test_cli_contracts_not_smoke.py
@@ -14,7 +14,7 @@ def test_calibrate_rejects_mixed_input_styles(tmp_path: Path):
     vm.write_text("point_name,E,N\np1,0,0\np2,1,0\np3,0,1\np4,1,1\n", encoding="utf-8")
     odr.write_text("<OpenDRIVE></OpenDRIVE>", encoding="utf-8")
 
-    # Mix two styles intentionally -> should error (logic is in calibrate.py) [2](blob:https://www.microsoft365.com/c655cd7d-9ac4-4928-84e7-b9a8f04405bd)
+    # Mix two styles intentionally -> should error (logic is in calibrate.py)
     res = run_cosmo(
         ["calibrate", "--inputs", str(pp), str(vm), str(odr), "--pixel-pairs", str(pp)],
         cwd=tmp_path,
@@ -27,7 +27,7 @@ def test_convert_rejects_positional_and_flag_input(tmp_path: Path):
     ol = tmp_path / "openlabel.json"
     ol.write_text(json.dumps({"openlabel": {"objects": {}, "frames": {}}}), encoding="utf-8")
 
-    # convert.py rejects positional + --input together [1](blob:https://www.microsoft365.com/3377b2c7-ce90-4a5f-bcf4-96fccf281101)
+    # convert.py rejects positional + --input together
     res = run_cosmo(["convert", str(ol), "--input", str(ol), "--no-mcap"], cwd=tmp_path)
     assert res.returncode != 0
     assert "Provide either a positional input OR --input/--openlabel" in (res.stderr + res.stdout)
diff --git a/tests/test_cli_smoke_calibrate.py b/tests/test_cli_smoke_calibrate.py
index 30da43d..423a823 100644
--- a/tests/test_cli_smoke_calibrate.py
+++ b/tests/test_cli_smoke_calibrate.py
@@ -14,7 +14,7 @@ def test_cli_calibrate_smoke(tmp_path: Path):
     Smoke test for the real CLI:
       cosmo calibrate --inputs pixel_pairs.csv visual_markers.csv map.xodr --json
 
-    Uses --inputs style and --json output exactly as supported by cosmo.cli.calibrate. [3](blob:https://www.microsoft365.com/c655cd7d-9ac4-4928-84e7-b9a8f04405bd)
+    Uses --inputs style and --json output exactly as supported by cosmo.cli.calibrate.
     """
     # Minimal input CSVs
     pixel_pairs_csv = tmp_path / "pixel_pairs.csv"
@@ -39,7 +39,7 @@ def test_cli_calibrate_smoke(tmp_path: Path):
         encoding="utf-8",
     )
 
-    # Dummy OpenDRIVE file (required arg in CLI contract) [3](blob:https://www.microsoft365.com/c655cd7d-9ac4-4928-84e7-b9a8f04405bd)
+    # Dummy OpenDRIVE file (required arg in CLI contract)
     odr_path = tmp_path / "map.xodr"
     odr_path.write_text("<OpenDRIVE></OpenDRIVE>", encoding="utf-8")
 
@@ -78,7 +78,7 @@ def test_cli_calibrate_smoke(tmp_path: Path):
 
     payload = extract_json_from_stdout(res.stdout)
 
-    # CLI prints asdict(result) when --json is provided. [3](blob:https://www.microsoft365.com/c655cd7d-9ac4-4928-84e7-b9a8f04405bd)
+    # CLI prints asdict(result) when --json is provided.
     run_dir = Path(payload["run_dir"])
     outputs_dir = Path(payload.get("outputs_dir") or payload["run_dir"])
     calib_path = Path(payload["calibration_json_path"])
diff --git a/tests/test_cli_smoke_convert.py b/tests/test_cli_smoke_convert.py
index 9bb1062..df7826d 100644
--- a/tests/test_cli_smoke_convert.py
+++ b/tests/test_cli_smoke_convert.py
@@ -14,7 +14,7 @@ def test_cli_convert_smoke_csv_only(tmp_path: Path):
     Smoke test for the real CLI:
       cosmo convert --input openlabel.json --calibration Calibration.json --no-mcap --json
 
-    Uses flags from cosmo.cli.convert and disables MCAP for CI stability. [1](blob:https://www.microsoft365.com/3377b2c7-ce90-4a5f-bcf4-96fccf281101)
+    Uses flags from cosmo.cli.convert and disables MCAP for CI stability.
     """
     # Minimal OpenLABEL input (one object, one frame, rbbox)
     openlabel = {
@@ -64,7 +64,7 @@ def test_cli_convert_smoke_csv_only(tmp_path: Path):
             str(out_dir),
             "--run-name",
             "smoke_convert",
-            "--no-mcap",  # convert CLI uses BooleanOptionalAction; --no-mcap disables MCAP. [1](blob:https://www.microsoft365.com/3377b2c7-ce90-4a5f-bcf4-96fccf281101)
+            "--no-mcap",  # convert CLI uses BooleanOptionalAction; --no-mcap disables MCAP.
             "--json",
         ],
         cwd=tmp_path,
diff --git a/tests/test_convert_alignment_flags.py b/tests/test_convert_alignment_flags.py
index 36ba79a..3f52b9a 100644
--- a/tests/test_convert_alignment_flags.py
+++ b/tests/test_convert_alignment_flags.py
@@ -29,4 +29,4 @@ def test_convert_accepts_alignment_flags(tmp_path: Path):
          "--no-mcap", "--swap-xy", "--flip-x", "--flip-y", "--xy-offset", "1.0", "-2.0", "--yaw-offset-deg", "90"],
         cwd=tmp_path,
     )
-    assert res.returncode == 0  # should be accepted and run successfully [3](blob:https://www.microsoft365.com/3377b2c7-ce90-4a5f-bcf4-96fccf281101)
+    assert res.returncode == 0  # should be accepted and run successfully
diff --git a/tests/test_convert_cli_validation.py b/tests/test_convert_cli_validation.py
index d9d8f6e..ce24958 100644
--- a/tests/test_convert_cli_validation.py
+++ b/tests/test_convert_cli_validation.py
@@ -16,4 +16,4 @@ def test_convert_rejects_positional_and_flag_input(tmp_path: Path):
         cwd=tmp_path,
     )
     assert res.returncode != 0
-    assert "Provide either a positional input OR --input/--openlabel" in (res.stderr + res.stdout)  # emitted by ap.error [3](blob:https://www.microsoft365.com/3377b2c7-ce90-4a5f-bcf4-96fccf281101)
+    assert "Provide either a positional input OR --input/--openlabel" in (res.stderr + res.stdout)  # emitted by ap.error
diff --git a/tests/test_convert_outputs.py b/tests/test_convert_outputs.py
index a778def..6aa8355 100644
--- a/tests/test_convert_outputs.py
+++ b/tests/test_convert_outputs.py
@@ -32,4 +32,4 @@ def test_convert_no_csv_reports_no_csv_path(tmp_path: Path):
     )
     assert res.returncode == 0
     payload = extract_json_from_stdout(res.stdout)
-    assert payload.get("csv_path") in (None, "", False)  # run_convert should reflect csv disabled [3](blob:https://www.microsoft365.com/3377b2c7-ce90-4a5f-bcf4-96fccf281101)
+    assert payload.get("csv_path") in (None, "", False)  # run_convert should reflect csv disabled