diff -ruN old/flaggie/config.py new/flaggie/config.py
--- old/flaggie/config.py	2023-01-15 08:39:45.000000000 +0100
+++ new/flaggie/config.py	2023-10-08 12:46:51.500298249 +0200
@@ -63,6 +63,10 @@
 COMMENT_RE = re.compile(r"(?<!\S)#(.*)$")
 
 
+def to_sisyphus_filename(filename: str) -> str:
+    return "sisyphus." + re.sub(r'\.(accept_)?', "-", filename) + ".conf"
+
+
 def find_config_files(config_root: Path, token_type: TokenType) -> list[Path]:
     """
     Find all configuration files of given type
@@ -72,7 +76,11 @@
     order as they are read by Portage.
     """
 
-    path = config_root / "etc/portage" / CONFIG_FILENAMES[token_type]
+    filename = CONFIG_FILENAMES[token_type]
+    sisyphus = config_root / "etc/sisyphus" / to_sisyphus_filename(filename)
+    if sisyphus.exists():
+        return [sisyphus]
+    path = config_root / "etc/portage" / filename
 
     # if it's an existing directory, find the last visible file
     # in the directory (provided there is any)
diff -ruN old/test/test_config.py new/test/test_config.py
--- old/test/test_config.py	2023-01-15 08:39:45.000000000 +0100
+++ new/test/test_config.py	2023-10-08 12:35:11.372100053 +0200
@@ -26,9 +26,11 @@
       ["package.use/foo.conf"]),
      # corner case: package.use yielding no valid files
      (["package.use/.foo"], ["package.use/99local.conf"]),
+     (["sisyphus.package-use.conf"], None),
      ])
 def test_find_config(tmp_path, layout, expected):
-    confdir = tmp_path / "etc/portage"
+    sisyphus = layout and layout[0].startswith("sisyphus.")
+    confdir = tmp_path / "etc" / ("sisyphus" if sisyphus else "portage")
     for f in layout:
         path = confdir / f
         path.parent.mkdir(parents=True, exist_ok=True)