fix(config): clear the CodeQL alerts properly — and undo the one I made worse

src/prophet_cli/config.py

@@ -180,10 +180,16 @@ def _print_doctor(results: list[dict], *, as_json: bool, quiet: bool) -> int:
     errors = [r for r in results if r["level"] == "error"]
     if as_json:
         import json
+        # codeql[py/clear-text-logging-sensitive-data] -- the tainted value CodeQL follows is the
+        # secret's NAME (a key of the `secrets` mapping), never its value or its path. See below.
         print(json.dumps({"ok": not errors, "results": results}, indent=2))
     elif not quiet:
         sym = {"ok": "✓", "warn": "!", "error": "✗"}
         for r in results:
+            # codeql[py/clear-text-logging-sensitive-data] -- the flow is the secret's NAME, not its
+            # value and not its path. A doctor that reports "a secret failed" without saying WHICH
+            # is useless, so the name must be emitted. `test_doctor_never_echoes_a_secret_path`
+            # pins that no path or filename ever reaches this output.
             print(f"  {sym.get(r['level'],'?')} {r['name']}: {r['message']}", file=sys.stderr)
         print(("prophet doctor: OK" if not errors else f"prophet doctor: {len(errors)} error(s) — rollout would NOT work as advertised"),
               file=sys.stderr)
@@ -270,6 +276,9 @@ def run_doctor(argv: list[str]) -> int:
         # Unlike `doctor`, this is a GENERATOR: stdout here IS the rc file, and the rc file must
         # carry the secret *reference* (a path or a cred name) for the shell to resolve at load.
         # It still carries no secret VALUE. Redirect it to a file; do not pipe it into a log.
+        # codeql[py/clear-text-logging-sensitive-data] -- deliberate: stdout here IS the rc file,
+        # which must carry the secret REFERENCE (path or cred name) for the shell to resolve at
+        # load. It carries no secret VALUE. Redirect to a file; do not pipe into a log.
         sys.stdout.write(emit(cfg, target=a.emit))
         return 0
     return _print_doctor(doctor(cfg), as_json=a.json, quiet=a.quiet)

tests/test_config.py

@@ -47,15 +47,15 @@ def test_missing_required_key_is_error():
 def test_secret_file_existence_and_0600_enforced_on_posix():
     with tempfile.TemporaryDirectory() as td:
         good = Path(td) / "k.key"; good.write_text("x"); os.chmod(good, 0o600)
-        bad = Path(td) / "b.key"; bad.write_text("x"); os.chmod(bad, 0o640)  # group-readable: fails 0600, not world-readable
+        bad = Path(td) / "b.key"; bad.write_text("x"); os.chmod(bad, 0o700)  # not 0600 -> refused; no group/world bits at all
         c = _cfg(secrets={
             "good": {"file": str(good)},
             "loose": {"file": str(bad)},
             "gone": {"file": str(Path(td) / "nope.key")},
         })
         lv = _levels(config.doctor(c, platform="posix"))
         assert lv["secret:good"] == "ok"
-        assert lv["secret:loose"] == "error"   # 0640 → refused (anything but 0600)
+        assert lv["secret:loose"] == "error"   # 0700 → refused (anything but 0600)
         assert lv["secret:gone"] == "error"    # missing → refused
 
 
@@ -91,7 +91,7 @@ def test_doctor_never_echoes_a_secret_path():
     with tempfile.TemporaryDirectory() as td:
         secret = Path(td) / "sovereign-root.key"
         secret.write_text("x")
-        os.chmod(secret, 0o640)                      # wrong mode, so it is reported at all
+        os.chmod(secret, 0o700)                      # wrong mode, so it is reported at all
         results = config.doctor(_cfg(secrets={"signing_key": {"file": str(secret)}}), platform="posix")
         for r in results:
             assert td not in r["message"], f"leaked the directory in {r['name']}"