[recipes] entity-wiki: emit real wikilinks and clickable thought-citation links in compiled wikis

[araece]

Problem

Compiled wikis contain no link syntax at all. The synthesis prompt never asks the LLM for links, and the LLM never sees target filenames (slugs are computed later, at write time), so:

• Relationships sections are inert plain text — in Obsidian, nothing on an entity page is navigable (- Claude Code (support: 3) is just text).
• [#thought-id] citations aren't clickable — and Obsidian misparses them as #tags, flooding the tag pane with meaningless hex tags.

Changes to generate-wiki.mjs

Deterministic Relationships rendering. The section is now rendered in script code from the structured typed_edges_by_relation data the script already builds, computing each target's slug with the same slugify() used for output filenames — so links are guaranteed to match real (or future) page names, with zero LLM involvement in the mechanical part. Bullets become - [[slug|Name]] (support: N). The system prompt tells the model to omit the section, and any LLM-emitted copy is stripped defensively.

Citation linkification. [#thought-id] refs — 8-char prefixes, full UUIDs, and multi-ref brackets like [#a, #b] (all three shapes observed in real output) — are rewritten into markdown links via a configurable URL template (--citation-url-template / OB_WIKI_CITATION_URL_TEMPLATE, must contain a <uuid> placeholder; a Supabase table-editor deep link works well). Resolution is scoped to each entity's own provenance ids; unresolvable or ambiguous refs stay untouched. There is deliberately no built-in default (project ref / table id are deployment-specific) — when unset, citations remain plain text. Re-running on already-linkified text is a no-op.

New retrofit scripts (for existing vaults, no recompile needed)

• retrofit-links.mjs — rewrites Relationships bullets into [[wikilinks]] where the target page exists. Unique-name matching with full-token extraction (never prefix matching), collision-safe: ambiguous names are left plain unless a (type) annotation disambiguates. Backs the vault up first.
• retrofit-citations.mjs — resolves citation ids against the thoughts table via PostgREST and links them with the same URL template. Deleted/ambiguous ids are left plain and counted. Verifies against the backup that only citation wrappers changed.

Tested

Run against a real 83-page compiled vault (~1,250 citations): 61 relationship links and 1,234 citation links added, 100% of emitted link targets resolve, and a byte-level diff confirmed the only changes anywhere are the link wrappers. node --check passes on all touched scripts. Idempotency re-run: 0 changes.

🤖 Generated with Claude Code

[github-actions]

Hey @araece — welcome to Open Brain Source! 👋

Thanks for submitting your first PR. The automated review will run shortly and check things like metadata, folder structure, and README completeness. If anything needs fixing, the review comment will tell you exactly what.

Once the automated checks pass, a human admin will review for quality and clarity. Expect a response within a few days.

If you have questions, check out CONTRIBUTING.md or open an issue.

[github-actions]

OB1 PR Gate

✅ Folder structure — All files are in allowed directories
✅ Required files — README.md and metadata.json found in all contribution folders
✅ Metadata valid — All metadata.json files passed JSON Schema validation
✅ No credentials — No API keys, tokens, or secrets detected
✅ SQL safety — No destructive SQL or core table modifications
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✅ README completeness — All READMEs include Prerequisites, Steps, and Expected Outcome
✅ Contribution dependencies — All declared skill and primitive dependencies exist and are linked in README
✅ LLM clarity review — Covered by Claude PR Review workflow
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✅ Tool audit link — Extensions/integrations link to the MCP Tool Audit guide
✅ Scope check — All changes are within the contribution folder(s)
✅ Internal links — All relative links in READMEs resolve to existing files

Result: All 15 checks passed! Ready for human review.

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Post-Merge Tasks

These don't block merge — they're reminders for admins after this PR lands.

• Add Entity Wiki Pages to recipes/README.md
• Add Alan Shurafa (@alanshurafa) to CONTRIBUTORS.md
• Post in OB1 Discord #show-and-tell