repro: fix bug in _get_active_graph (#3301)

We are currently removing all of the deps stages from the DAG even if
those deps are referenced by some parallel branches of execution.
The new approach is to remove edges and then gradually remove nodes if
there are no more `in` edges left.

Discord context:
https://discordapp.com/channels/485586884165107732/485596304961962003/676464313942409265

tests/unit/repo/test_repo.py

@@ -0,0 +1,51 @@
+import os
+
+import pytest
+
+
+def test_is_dvc_internal(dvc):
+    assert dvc.is_dvc_internal(os.path.join("path", "to", ".dvc", "file"))
+    assert not dvc.is_dvc_internal(os.path.join("path", "to-non-.dvc", "file"))
+
+
+@pytest.mark.parametrize(
+    "path",
+    [
+        os.path.join("dir", "subdir", "file"),
+        os.path.join("dir", "subdir"),
+        "dir",
+    ],
+)
+def test_find_outs_by_path(tmp_dir, dvc, path):
+    stage, = tmp_dir.dvc_gen(
+        {"dir": {"subdir": {"file": "file"}, "other": "other"}}
+    )
+
+    outs = dvc.find_outs_by_path(path, strict=False)
+    assert len(outs) == 1
+    assert outs[0].path_info == stage.outs[0].path_info
+
+
+@pytest.mark.parametrize(
+    "path",
+    [os.path.join("dir", "subdir", "file"), os.path.join("dir", "subdir")],
+)
+def test_used_cache(tmp_dir, dvc, path):
+    from dvc.cache import NamedCache
+
+    tmp_dir.dvc_gen({"dir": {"subdir": {"file": "file"}, "other": "other"}})
+    expected = NamedCache.make(
+        "local", "70922d6bf66eb073053a82f77d58c536.dir", "dir"
+    )
+    expected.add(
+        "local",
+        "8c7dd922ad47494fc02c388e12c00eac",
+        os.path.join("dir", "subdir", "file"),
+    )
+
+    with dvc.state:
+        used_cache = dvc.used_cache([path])
+        assert (
+            used_cache._items == expected._items
+            and used_cache.external == expected.external
+        )