diff --git a/tests/test_clean_input_selection.py b/tests/test_clean_input_selection.py
index 6e75431..b527a3a 100644
--- a/tests/test_clean_input_selection.py
+++ b/tests/test_clean_input_selection.py
@@ -177,6 +177,67 @@ def test_run_clean_uses_manifest_primary(tmp_path: Path, monkeypatch):
     assert seen["input_files"] == [selected_file]
 
 
+def test_run_clean_mode_all_ignores_manifest_primary(tmp_path: Path, monkeypatch):
+    raw_dir = tmp_path / "data" / "raw" / "demo" / "2024"
+    raw_dir.mkdir(parents=True, exist_ok=True)
+    first_file = raw_dir / "a.csv"
+    first_file.write_text("a\n1\n", encoding="utf-8")
+    second_file = raw_dir / "b.csv"
+    second_file.write_text("a\n2\n", encoding="utf-8")
+    write_raw_manifest(
+        raw_dir,
+        {
+            "dataset": "demo",
+            "year": 2024,
+            "run_id": "run-1",
+            "created_at": "2026-02-28T00:00:00+00:00",
+            "sources": [{"name": "source_1", "output_file": "a.csv"}],
+            "primary_output_file": "a.csv",
+        },
+    )
+
+    sql_path = _write_clean_sql(tmp_path)
+    seen = _run_clean_capture_inputs(
+        monkeypatch,
+        tmp_path,
+        {"sql": str(sql_path), "read": {"mode": "all"}},
+    )
+
+    assert seen["input_files"] == [first_file, second_file]
+
+
+def test_run_clean_explicit_include_ignores_manifest_primary(tmp_path: Path, monkeypatch):
+    raw_dir = tmp_path / "data" / "raw" / "demo" / "2024"
+    raw_dir.mkdir(parents=True, exist_ok=True)
+    preferred_file = raw_dir / "preferred.csv"
+    preferred_file.write_text("a\n1\n", encoding="utf-8")
+    target_file = raw_dir / "uscite.csv"
+    target_file.write_text("a\n2\n", encoding="utf-8")
+    write_raw_manifest(
+        raw_dir,
+        {
+            "dataset": "demo",
+            "year": 2024,
+            "run_id": "run-1",
+            "created_at": "2026-02-28T00:00:00+00:00",
+            "sources": [{"name": "source_1", "output_file": "preferred.csv"}],
+            "primary_output_file": "preferred.csv",
+        },
+    )
+
+    sql_path = _write_clean_sql(tmp_path)
+    seen = _run_clean_capture_inputs(
+        monkeypatch,
+        tmp_path,
+        {
+            "sql": str(sql_path),
+            "read": {"mode": "explicit", "include": ["uscite.csv"]},
+        },
+    )
+
+    assert seen["input_files"] == [target_file]
+
+
 def test_run_clean_rejects_php_only_inputs_with_clear_error(tmp_path: Path):
     raw_dir = tmp_path / "data" / "raw" / "demo" / "2024"
     raw_dir.mkdir(parents=True, exist_ok=True)
diff --git a/toolkit/clean/input_selection.py b/toolkit/clean/input_selection.py
index 222ba8c..c239cbb 100644
--- a/toolkit/clean/input_selection.py
+++ b/toolkit/clean/input_selection.py
@@ -138,6 +138,14 @@ def _manifest_primary_input(raw_year_dir: Path) -> tuple[Path | None, str | None
     )
 
 
+def _should_use_manifest_primary(mode: str, include=None) -> bool:
+    if mode == "all":
+        return False
+    if mode == "explicit" and include is not None:
+        return False
+    return True
+
+
 def select_raw_input(
     raw_year_dir: Path,
     logger,
@@ -165,11 +173,12 @@ def select_raw_input(
                 prefer_from_raw_run=prefer_from_raw_run,
             )
 
-    manifest_primary, manifest_warning = _manifest_primary_input(raw_year_dir)
-    if manifest_primary is not None:
-        return [manifest_primary]
-    if manifest_warning is not None:
-        logger.warning(manifest_warning)
+    if _should_use_manifest_primary(mode, include=include):
+        manifest_primary, manifest_warning = _manifest_primary_input(raw_year_dir)
+        if manifest_primary is not None:
+            return [manifest_primary]
+        if manifest_warning is not None:
+            logger.warning(manifest_warning)
 
     selected = select_inputs(
         selected_candidates,