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Research-Stack/6-Documentation/docs/OBSIDIAN_INTEGRATION.md

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Obsidian Integration

Status: local vault configured as an audit/shim surface.

Local Vault

Default vault path:

/home/allaun/Documents/Research Stack/Obdisidan connector

The name reflects the existing local folder. It can be renamed later, but the current configuration preserves the working vault path instead of moving user data.

Lake

Default JSON-L lake:

/home/allaun/Documents/Research Stack/data/obsidian_lake.jsonl

Obsidian notes are stored as informational_bind entries with path, title, tags, links, content hash, content preview, and full markdown content.

Commands

Ingest local vault into the lake:

python3 scripts/obsidian_sync_shim.py ingest --backend local

Two-way local sync with Obsidian winning conflicts:

python3 scripts/obsidian_sync_shim.py sync --backend local

Export lake entries back to the vault without overwriting existing notes:

python3 scripts/obsidian_sync_shim.py export --backend local

Use the topological engine when it is online, otherwise fall back to the local vault:

python3 scripts/obsidian_sync_shim.py sync --backend auto

Boundaries

  • Obsidian is an audit and navigation surface.
  • ENE/JSON-L remains the durable substrate for ingested notes.
  • Notion and Linear remain tracker/publication surfaces.
  • Lean remains the source of truth for formal math and invariants.
  • No secrets belong in Obsidian notes.

Related Surfaces

  • scripts/obsidian_sync_shim.py
  • infra/topological_engine_client.py
  • data/obsidian_lake.jsonl
  • docs/MCP_NOTION_LINEAR_SETUP.md
  • docs/AGENTS.md