diff --git a/src/coretrace_python/engine.py b/src/coretrace_python/engine.py
index 98f63a8..c951d6e 100644
--- a/src/coretrace_python/engine.py
+++ b/src/coretrace_python/engine.py
@@ -384,6 +384,12 @@ def analyze_project(
 
     if jobs < 1:
         raise ValueError("jobs must be at least 1")
+    # Module sources are loaded by their resolved path; every other file the project is
+    # read from (manifests, configuration, advisories, policy) must be named the same way,
+    # or the reports and baselines would see it relative to the working directory (#206).
+    root = root.resolve()
+    advisory_files = [path.resolve() for path in advisory_files]
+    policy_file = None if policy_file is None else policy_file.resolve()
     sources = SourceManager()
     findings: list[Finding] = []
     dependencies = resolve_dependencies(root, sources)
diff --git a/tests/test_relative_root.py b/tests/test_relative_root.py
new file mode 100644
index 0000000..276e525
--- /dev/null
+++ b/tests/test_relative_root.py
@@ -0,0 +1,111 @@
+"""Acceptance tests for issue #206: a root given as a relative path.
+
+Findings located in a dependency file or a configuration file are reported relative to
+the analysed root, like the findings of Python modules, whatever the working directory
+and whether the root was given as a relative or an absolute path. A baseline recorded
+with one form of the root therefore matches the findings of a check with the other.
+"""
+
+from __future__ import annotations
+
+import json
+from pathlib import Path
+
+import pytest
+
+from coretrace_python.cli import main
+from coretrace_python.dependency import Advisory, dump_advisories
+from coretrace_python.findings import Severity
+
+LOCK = """\
+version = 1
+
+[[package]]
+name = "vulnlib"
+version = "1.0.0"
+source = { registry = "https://pypi.org/simple" }
+"""
+ADVISORY = Advisory("CVE-2099-0206", "vulnlib", "<1.1", "vulnlib is vulnerable", Severity.MEDIUM)
+SETTINGS = '{"api_token": "Zx81kQpLw0RtY7vBn3MsD9cF2hJ6gK4a"}\n'
+
+
+@pytest.fixture
+def project(tmp_path: Path, monkeypatch: pytest.MonkeyPatch) -> Path:
+    """A project ``proj`` under the working directory, with a vulnerable locked
+    requirement and a credential in a configuration file."""
+
+    root = tmp_path / "proj"
+    root.mkdir()
+    (root / "uv.lock").write_text(LOCK, encoding="utf-8")
+    (root / "advisories.json").write_text(dump_advisories((ADVISORY,)), encoding="utf-8")
+    (root / "settings.json").write_text(SETTINGS, encoding="utf-8")
+    (root / "app.py").write_text("import vulnlib\n", encoding="utf-8")
+    monkeypatch.chdir(tmp_path)
+    return root
+
+
+def located(capsys: pytest.CaptureFixture[str], rule: str) -> list[str]:
+    report = json.loads(capsys.readouterr().out)
+    return sorted(f["location"]["path"] for f in report["findings"] if f["rule_id"] == rule)
+
+
+@pytest.mark.parametrize("form", ["relative", "absolute"])
+def test_dependency_findings_are_located_relative_to_the_root(
+    project: Path, form: str, capsys: pytest.CaptureFixture[str]
+) -> None:
+    root = "proj" if form == "relative" else str(project)
+
+    main(["--check", root, "--format", "json"])
+
+    assert located(capsys, "vulnerable-dependency") == ["uv.lock"]
+
+
+@pytest.mark.parametrize("form", ["relative", "absolute"])
+def test_configuration_findings_are_located_relative_to_the_root(
+    project: Path, form: str, capsys: pytest.CaptureFixture[str]
+) -> None:
+    root = "proj" if form == "relative" else str(project)
+
+    main(["--check", root, "--format", "json"])
+
+    assert located(capsys, "hardcoded-credential") == ["settings.json"]
+
+
+@pytest.mark.parametrize(
+    ("option", "name", "text"),
+    [
+        ("--policy", "bad-policy.toml", "[dependencies\n"),
+        ("--advisories", "bad-advisories.json", "{\n"),
+    ],
+)
+def test_explicit_files_are_located_relative_to_the_root(
+    project: Path, option: str, name: str, text: str, capsys: pytest.CaptureFixture[str]
+) -> None:
+    (project / name).write_text(text, encoding="utf-8")
+
+    main(["--check", "proj", option, f"proj/{name}", "--format", "json"])
+
+    assert located(capsys, "syntax-error") == [name]
+
+
+@pytest.mark.parametrize("form", ["relative", "absolute"])
+def test_a_root_reached_through_a_symbolic_link_keeps_root_relative_paths(
+    project: Path, tmp_path: Path, form: str, capsys: pytest.CaptureFixture[str]
+) -> None:
+    (tmp_path / "link").symlink_to(project, target_is_directory=True)
+    root = "link" if form == "relative" else str(tmp_path / "link")
+
+    main(["--check", root, "--format", "json"])
+
+    assert located(capsys, "vulnerable-dependency") == ["uv.lock"]
+
+
+def test_a_baseline_recorded_with_a_relative_root_matches_an_absolute_one(
+    project: Path, tmp_path: Path, capsys: pytest.CaptureFixture[str]
+) -> None:
+    baseline = tmp_path / "baseline.json"
+    assert main(["--check", "proj", "--baseline", str(baseline)]) == 0
+    capsys.readouterr()
+
+    assert main(["--check", str(project), "--baseline", str(baseline)]) == 0
+    assert capsys.readouterr().out.startswith("no findings, 2 baselined\n")