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

[szsip239]

Problem

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.

Repro

graphify <path> --wiki              # generates ~100 articles + index
graphify <path> --update --wiki     # generates ~100 NEW articles (LLM picks different names)
ls graphify-out/wiki/*.md | wc -l   # ~200 files, index references ~100
# Repeat → unbounded growth

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.

out.mkdir(parents=True, exist_ok=True)

# NEW: prevent orphan accumulation
for old_article in out.glob("*.md"):
    old_article.unlink()

Tests

Two new regression tests in tests/test_wiki.py:

1. test_to_wiki_clears_stale_articles — calls to_wiki() twice with different community labels, asserts old files are gone and new files exist.
2. test_to_wiki_preserves_non_md_files — places PNG/JSON/subdirectory content in the wiki dir, asserts they survive cleanup.

All 17 tests in test_wiki.py pass (15 existing + 2 new).

Compatibility

• No CLI / API change
• No behavioral change for first-time wiki generation (empty dir → no .md files to clear)
• Custom .md files placed at top level of wiki/ (not a documented workflow) would be removed on next --wiki. Subdirectories and non-.md files are unaffected.

Related work

Existing wiki improvements addressed adjacent concerns but not orphan cleanup:

• [skill] --wiki flag has no implementation step: running after Step 9 cleanup silently loses community labels #229 — wiki labels persistence (.graphify_labels.json)
• Emit wiki/ on code-only rebuild so report wikilinks resolve #382 — emit wiki on code-only rebuild
• Feature request: post-commit hook should optionally rebuild the wiki #549 — post-commit hook with wiki rebuild