HivemindOS manual

Where Hive Superbrain keeps things

Your Hive Superbrain is a normal Obsidian vault. You only need to know where your own notes go; HivemindOS looks after its indexes and service files.

The folders you will use

Folder	Put this here
`Intake/`	New, unsorted material: captures, requests, source files, and voice notes.
`Memory/`	Notes worth keeping: decisions, meetings, briefings, imported sources, and conversation history.
`Ideas/`	Your own questions, taste, mental models, and early thinking.
`Projects/`	Active project context, plans, status updates, and decisions.
`Synthesis/`	Drafts, research summaries, and compiled knowledge made from sources.
`Skills/`	Reusable instructions that teach agents a workflow.
`Archive/`	Finished, inactive, or deliberately preserved material.

Operations/ belongs mostly to HivemindOS: schedules, health records, notifications, and other working state. You can look inside, but don’t hand-edit it unless a repair guide tells you to.

How new material moves

New material usually lands in Intake/. Once reviewed, it becomes project context, a memory, an idea, or a synthesis note. A repeatable method belongs in Skills/, not in a project note. Agents follow the same map, so a note one agent writes is easy for the next to find.

Your regular Markdown notes are yours to rename, link, and edit in Obsidian. For HivemindOS working data, use the dashboard or the repair commands in Sync and repair.

Open the complete folder and storage reference

Directory Structure

A clean HivemindOS vault looks roughly like this. Project, skill, and migration folders vary; the top level should not.

hivemindos-vault/
|-- AGENTS.md
|-- Shared Context.md
|-- .hivemindos-transfers/
|   `-- <handoff-transfer-id>/
|-- Intake/
|   |-- Requests/
|   `-- Sources/
|-- Memory/
|   |-- Core Memory.md
|   |-- Book Notes/
|   |-- Conversations/
|   |   `-- <agent-name>/
|   |       `-- YYYY-MM-DD-<title>-<sessionId>.md
|   |-- Daily Briefings/
|   |-- Decision Journal/
|   |-- Distillations/
|   |   `-- Agent Memory/
|   |       |-- <type>/                  (shared memories)
|   |       |-- Agents/<agent-id>/       (one agent's private memories)
|   |       |   `-- Core Memory.md
|   |       `-- Tasks/<task-id>/         (notes shared by one task's agents)
|   |-- Imported Sources/
|   |-- Meetings/
|   `-- Weekly Reviews/
|-- Synthesis/
|   |-- raw/
|   |-- wiki/
|   |   |-- .drafts/
|   |   |-- queries/
|   |   |-- sources/
|   |   `-- synthesis/
|   `-- pack/
|-- Ideas/
|-- Projects/
|-- Operations/
|   |-- AI-Ready Vault Contract.md
|   |-- Agent Notifications/
|   |-- Automations/
|   |   |-- Foundation Workflows/
|   |   `-- Project Autopilot/
|   |-- Brain Services/
|   |   |-- Agent Memory.base
|   |   |-- Agent Memory Proofs.jsonl (optional receipts)
|   |   |-- Conversations Index.jsonl
|   |   |-- Full Vault Search Index.md
|   |   |-- GBrain.md
|   |   |-- Neo4j.md
|   |   |-- Obsidian CLI.md
|   |   |-- Obsidian Native Brain Pack.md
|   |   |-- Obsidian Plugin Pack.md
|   |   |-- Project Brain.base
|   |   |-- QMD.md
|   |   |-- Queen Bee/
|   |   |   |-- Identity.md
|   |   |   |-- Routing Policy.md
|   |   |   |-- Safety Policy.md
|   |   |   |-- intent-dedupe.jsonl
|   |   |   |-- leases.jsonl
|   |   |   `-- receipts.jsonl
|   |   |-- Secure References.base
|   |   |-- Hive Superbrain.canvas
|   |   `-- Syntho.md
|   |-- Code Projects/
|   |-- Runtime Mirrors/
|   |   `-- AEON/
|   |       `-- .aeon/
|   |-- Secure/
|   |-- Vault Migrations/
|   `-- Work Board/
|-- Skills/
|   |-- README.md
|   `-- <skill-slug>/
|       `-- SKILL.md
|-- Templates/
|   `-- HivemindOS/
`-- Archive/
    `-- Processed Requests/

Search indexes and their history are not in the vault. Each device builds its own from the notes and keeps them in its HivemindOS folder, so sync only ever carries notes:

~/.hivemindos/brain/state/<vault-id>/Operations/Brain Services/
|-- Agent Memory Index.jsonl
|-- Agent Memory Entity Index.jsonl
|-- Agent Memory Retrievals.jsonl
|-- Agent Memory Transactions.jsonl
|-- Agent Memory Embeddings.jsonl (when embeddings are on)
|-- Full Vault Search Index.jsonl
`-- Index Generations/
    |-- agent-memory/
    |   |-- coverage.json (after history is pruned)
    |   `-- <generation-id>/
    `-- full-vault/
        |-- coverage.json (after history is pruned)
        `-- <generation-id>/

Folder jobs

Folder	Purpose
`Intake/`	Raw captures, requests, web clips, voice notes, and unsorted sources.
`.hivemindos-transfers/`	Hivemind Sync handoff files between trusted machines. Never store secrets here.
`Memory/`	Durable knowledge: briefings, reviews, decisions, meetings, imported sources, distillations, and conversation notes. `Memory/Core Memory.md` is the short note every agent session starts with.
`Memory/Conversations/`	One redacted note per finished chat, grouped by agent.
`Synthesis/`	Drafts, research summaries, reviewed analysis, and agent output.
`Ideas/`	Your original thinking, questions, and strategy.
`Projects/`	Active work, plans, status, and decisions.
`Operations/Automations/`	Scheduler records and foundation workflow schedules.
`Operations/Work Board/`	Work Board state.
`Operations/Agent Notifications/`	Shared notifications.
`Operations/Brain Services/`	Service notes (QMD, GBrain, Neo4j, Syntho, and others), the conversation index, and optional receipts.
`Operations/Brain Services/Queen Bee/`	Queen Bee policy, state, dedupe records, leases, and receipts.
`Operations/Secure/`	Encrypted backups and key-name status notes only. No plaintext secrets.
`Operations/Runtime Mirrors/`	Runtime working copies, such as the hidden AEON `.aeon` mirror.
`Operations/Vault Migrations/`	Cleanup manifests and archived duplicates or conflicts.
`Skills/`	Shared agent procedures: `Skills/README.md`, then `Skills/<slug>/SKILL.md`.
`Templates/HivemindOS/`	Note templates with consistent metadata.
`Archive/`	Completed, inactive, or processed material.

Seeded child paths

Setup creates these because agents and workflows expect them:

Intake/Requests, Intake/Sources
Memory/Daily Briefings, Memory/Weekly Reviews, Memory/Imported Sources, Memory/Conversations, Memory/Distillations, Memory/Distillations/Agent Memory
Operations/Automations, Operations/Work Board, Operations/Agent Notifications, Operations/Brain Services, Operations/Secure, Operations/Runtime Mirrors
Memory/Core Memory.md, a short template for your standing context
Operations/Brain Services/Agent Memory.base, Full Vault Search Index.md, Neo4j.md, Project Brain.base, Secure References.base, Hive Superbrain.canvas
Templates/HivemindOS
Archive/Processed Requests

Where memory lives

Typed memories: Memory/Distillations/Agent Memory/. These notes are the source; the indexes are generated from them and rebuildable.
Memory layers: shared memories sit in the type folders; one agent’s private memories in Agents/<agent-id>/; notes shared by the agents on one Work Board task in Tasks/<task-id>/. See Memory layers.
Core memory: Memory/Core Memory.md, plus an optional Core Memory.md in an agent’s own folder.
Search indexes, on each device: Agent Memory Index.jsonl, Agent Memory Entity Index.jsonl, Agent Memory Retrievals.jsonl, and Full Vault Search Index.jsonl (described in Full Vault Search Index.md), under ~/.hivemindos/brain/state/<vault-id>/Operations/Brain Services/.
Verified index history, on each device: Index Generations/ beside those indexes, with a coverage.json per index after pruning.
Write recovery journal, on each device: Agent Memory Transactions.jsonl in the same folder.
Optional hash-only receipts, in the vault: Operations/Brain Services/Agent Memory Proofs.jsonl.
Optional service notes: QMD.md, GBrain.md, and Neo4j.md in Operations/Brain Services/. Connection values stay in env keys, never in notes.
Conversation index: Operations/Brain Services/Conversations Index.jsonl.
Outside the vault: operational events in ~/.hivemindos/brain/operational-events.jsonl and portable capsules in ~/.hivemindos/brain/capsules/.

Agents reach memory through the app when it manages them and through hive-brain answer "<query>" otherwise. Claude Code also gets the hive-brain-hook prompt hook. See Memory and knowledge for details.

Retired folders

These should not be used as top-level folders. The vault doctor finds them and moves or archives them carefully:

Notes/, Inbox/, Scheduled/, agent-notifications/, kanban/, claw-code/, foo-empty/, .omni-sync-test/, and root pineapple-*.md files.