obsidian-orphan-rescue

name	obsidian-orphan-rescue
description	Fix Obsidian orphans at the source. Auto-link orphan notes in any [[wikilink]] markdown vault. Three modes: resolve (deterministic alias-table resolution, $0), anchor (local embedding fallback to nearest existing hub by cosine, $0), and mint (experimental, clusters orphans + mints new concept hubs). Safe-writes contract: frontmatter-only writes, atomic, idempotent, dangling-link guard, per-hub absorption cap, body-only content hash preserved, concepts-only by default. Use when the user asks any of: fix my obsidian orphans, obsidian orphan notes, auto-link my obsidian vault, obsidian unlinked notes, obsidian de-orphan, connect my obsidian notes, obsidian wikilink resolver, obsidian entity resolution, fix obsidian link rot, obsidian auto wikilink, anchor my orphans, obsidian orphan rescuer, rescue obsidian orphans, resolve obsidian entities, fix obsidian dangling links. Works on any markdown vault using [[wikilinks]] (Obsidian, Logseq, Foam, Quartz).
license	MIT
author	Dhiraj Singh Pawar (build-with-dhiraj)
homepage	https://github.com/build-with-dhiraj/obsidian-orphan-rescue
version	0.1.0

obsidian-orphan-rescue

Fix Obsidian orphans at the source. Auto-link orphan notes in any markdown vault that uses [[wikilinks]]. Frontmatter-only writes. Atomic. Idempotent.

When to use this skill

Trigger this skill whenever the user wants to:

1. Fix orphans, not just list them. Every other tool lists orphans; this one auto-fixes them with safety guards.
2. Resolve plain-string entities to wikilinks. A note tagged entities: [Microscopy] should become entities: [[[microscopy]]] if a microscopy hub exists.
3. De-orphan a leaf. Attach a true orphan to its single best matching existing hub by embedding cosine.
4. Mint hubs for coherent orphan clusters (experimental). For clusters of >= 5 orphans about the same topic, create a new concept hub and anchor them to it.

The three modes

Mode	What it does	Network?	Writes new notes?
resolve	Plain-string entities/topics → canonical [[wikilinks]] via alias table	No	No
anchor	True-orphan leaves → nearest existing hub by cosine similarity	No (local fastembed)	No
mint	Cluster orphans → mint new concept hubs (EXPERIMENTAL)	LLM naming call	YES (new hubs)

Safety guards (read this first)

Every other PKM auto-link tool stops here because writing to a vault is dangerous. The orphan-rescue's contract is what makes it safe:

• Frontmatter-only writes. Body bytes are never modified.
• Atomic writes. tempfile + os.rename, crash-safe; no partial writes.
• Body-only content hash preserved. Downstream embedders never re-embed.
• Idempotency stamps. A second run on unchanged notes is a no-op.
• Dangling-link guard. Only links to hubs that exist on disk.
• Per-hub absorption cap. No single hub can absorb more than N orphans per run (anti-star).
• Concepts-only target set by default. Generic how-tos never anchor to brand entity hubs (the brand-leak guard).