llm-wiki-obsidian-hardening

LLM-Wiki Obsidian Hardening

Goal

Make an Obsidian vault safer for agent-assisted LLM-Wiki work.

When to use

• Before letting a coding agent edit an Obsidian vault for the first time.
• When wikilinks, embeds, or attachment folders keep breaking after agent edits.
• When setting up AGENTS.md/CLAUDE.md boundaries for a vault used with LLM-Wiki workflows.
• When a vault syncs via iCloud, Syncthing, or Obsidian Sync and index or WAL files risk corruption.
• Before running bulk edits or migrations across vault notes.

Inputs

• Obsidian vault path.
• Desired mode: audit-only or apply.
• Sync method if known.
• Existing plugins and conventions if relevant.

Procedure

1. Preflight

Check:

• git or backup exists;
• .obsidian/ is present;
• attachment folders and embedded files;
• wikilink style;
• frontmatter style;
• existing AGENTS.md/CLAUDE.md;
• sync tool and local cache/index files;
• re-verify the vault's current file state immediately before applying changes, since sync tools may have modified files since the initial scan.

2. Protect Obsidian semantics

Ensure instructions say:

• preserve [[wikilinks]] unless user asks otherwise;
• do not rewrite embeds ![[...]];
• do not move attachments without link repair;
• do not cat the whole vault;
• use rg or Obsidian CLI when available;
• preserve comments, aliases and YAML quoting.

3. Add LLM-Wiki boundaries

Recommend or add:

raw/
wiki/
inbox/
_meta/
_agent/

Add protected section markers around human synthesis when useful.

4. Harden writes

Suggest:

• dry-run for bulk edits;
• git branch for migrations;
• frontmatter validation;
• no edits under raw/;
• wiki-lint after large changes;
• local-only handling for sensitive notes.

5. Sync and index policy

Flag dangerous patterns:

• syncing SQLite WAL/SHM files;
• syncing HNSW/vector index files;
• using multiple sync systems on one vault;
• treating generated indexes as source of truth.

Prefer per-device indexes and reconstructable caches.