fix(wiki): clear stale articles before regenerating to prevent orphan accumulation (#558)

to_wiki() writes a fresh set of community + god-node articles each call but
never deletes old files from previous runs. Since community labels are
LLM-generated and non-deterministic across rebuilds (per skill.md Step 5),
the same conceptual community is often named differently each time, leaving
its previous file as an orphan. After N rebuilds, wiki/ contains roughly N
times the active article count, with index.md only referencing the most
recent run's labels.

Real-world: a knowledge corpus accumulated 822 wiki .md files over 5
rebuilds, of which only 111 were referenced by index.md (710 orphans).

Fix: clear *.md files in the output directory at the start of to_wiki().
This is consistent with its existing fully-regenerative behavior — it
always writes the full set of articles + index, never partial updates.
Subdirectories and non-.md files are preserved (only top-level .md is
touched), so any user-placed auxiliary assets survive.

Tests: two new regression tests cover (1) stale article cleanup across
runs with different labels, and (2) preservation of non-.md user files
and nested subdirectories.

graphify/wiki.py

@@ -185,6 +185,15 @@ def to_wiki(
     out = Path(output_dir)
     out.mkdir(parents=True, exist_ok=True)
 
+    # Clear stale .md files from previous runs to prevent orphan accumulation.
+    # Community labels are LLM-generated (per skill.md Step 5) and non-deterministic
+    # across runs — the same conceptual community may be named differently each time
+    # (e.g. "AutoAgent Skills" → "AutoAgent Methodology"), leaving the previous file
+    # as an orphan. Since to_wiki() owns wiki/ entirely (always writes the full set),
+    # it can safely clear .md files at the start of each call.
+    for old_article in out.glob("*.md"):
+        old_article.unlink()
+
     labels = community_labels or {cid: f"Community {cid}" for cid in communities}
     cohesion = cohesion or {}
     god_nodes_data = god_nodes_data or []

tests/test_wiki.py

@@ -137,3 +137,50 @@ def test_community_article_truncation_notice(tmp_path):
     to_wiki(G, communities, tmp_path, community_labels={0: "Big Community"})
     article = (tmp_path / "Big_Community.md").read_text()
     assert "and 5 more nodes" in article
+
+
+def test_to_wiki_clears_stale_articles(tmp_path):
+    """Regression: previous-run articles must be removed when labels change.
+
+    Real-world impact: community labels are LLM-generated (per skill.md Step 5)
+    and non-deterministic across runs, so the same conceptual community gets a
+    different 2-5 word name each rebuild. Without cleanup, every rebuild leaves
+    the previous run's files as orphans, growing wiki/ unboundedly.
+    """
+    G = _make_graph()
+
+    # First run with one set of labels
+    to_wiki(G, COMMUNITIES, tmp_path, community_labels={0: "Old Name A", 1: "Old Name B"})
+    assert (tmp_path / "Old_Name_A.md").exists()
+    assert (tmp_path / "Old_Name_B.md").exists()
+
+    # Second run simulates LLM picking different names for the same communities
+    to_wiki(G, COMMUNITIES, tmp_path, community_labels={0: "New Name A", 1: "New Name B"})
+
+    # Old files should be gone; new files should exist
+    assert not (tmp_path / "Old_Name_A.md").exists(), "stale article from previous run not cleared"
+    assert not (tmp_path / "Old_Name_B.md").exists(), "stale article from previous run not cleared"
+    assert (tmp_path / "New_Name_A.md").exists()
+    assert (tmp_path / "New_Name_B.md").exists()
+    # index.md is always rewritten
+    assert (tmp_path / "index.md").exists()
+
+
+def test_to_wiki_preserves_non_md_files(tmp_path):
+    """Cleanup only touches top-level .md files; subdirectories and other files survive.
+
+    Some users may keep auxiliary assets (images, .json sidecars) in wiki/ —
+    cleanup must not be destructive beyond its own .md output domain.
+    """
+    G = _make_graph()
+    tmp_path.mkdir(parents=True, exist_ok=True)
+    (tmp_path / "user_image.png").write_bytes(b"\x89PNG fake")
+    (tmp_path / "user_data.json").write_text('{"key": "value"}')
+    (tmp_path / "subdir").mkdir()
+    (tmp_path / "subdir" / "nested.md").write_text("# user content")
+
+    to_wiki(G, COMMUNITIES, tmp_path, community_labels=LABELS)
+
+    assert (tmp_path / "user_image.png").exists(), "non-.md file deleted"
+    assert (tmp_path / "user_data.json").exists(), "non-.md file deleted"
+    assert (tmp_path / "subdir" / "nested.md").exists(), "subdirectory .md deleted"