feat(wiki): preserve hand-authored custom pages across export

[TomaszWu14]

Problem

graphify export wiki deletes every wiki/*.md at the start of each run:

for old_article in out.glob("*.md"):
    old_article.unlink()

This exists to clear orphaned community articles (LLM-generated labels are non-deterministic, so a renamed community would otherwise leave its old file behind). But it also deletes any page a user added by hand — custom analysis, notes, topology deep-dives — with no way to keep them. Re-running the export silently wipes them, and there's no opt-out.

Fix

to_wiki now tracks the files it generates in a .graphify_wiki_files.json manifest and, on re-export, deletes only its own prior output (files it generated last run but not this run — e.g. renamed communities). Any file graphify never wrote is left untouched.

Preserved pages are also auto-listed in a Custom Pages section of index.md, titled by their first markdown # H1 (falling back to a de-slugged filename), so they stay reachable from the agent entry point instead of becoming orphans.

Migration safety: the first run after upgrade has no manifest, so it deletes nothing — existing custom pages survive. Self-generated orphans are cleaned up from the next run onward.

Behavior

• Community/god-node articles regenerate exactly as before (byte-identical on an unchanged graph).
• A hand-authored my-analysis.md now survives re-export and appears under ## Custom Pages in the index.
• Renaming a community still removes its stale article (verified by test).

Tests

Adds 5 tests to tests/test_wiki.py:

• test_to_wiki_preserves_custom_pages
• test_index_lists_custom_pages_by_h1
• test_to_wiki_removes_only_its_own_orphans
• test_to_wiki_writes_manifest
• test_custom_page_without_h1_falls_back_to_filename

pytest tests/test_wiki.py → 35 passed (30 existing + 5 new).

Notes

• import json moved to module level (was needed by the new manifest read/write).
• No public API change; to_wiki's signature is unchanged. _index_md gains an optional custom_pages argument.

[TomaszWu14]

Friendly heads-up: this PR is a first-time contribution, so the CI workflows are sitting in action_required pending maintainer approval. Whenever a maintainer has a moment, could you approve the workflow run so the checks can execute? Happy to address anything they surface. Thanks for the great tool! 🙏