# hyperresearch | Jordan Gibbs | Knowledge Base | Instagit

Agent-driven research knowledge base. Agents collect, search, and synthesize web research into a persistent, searchable wiki.

GitHub Stars: 3k

Repository: https://github.com/jordan-gibbs/hyperresearch

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## Articles

### [How Hyperresearch Handles Open-Access Recovery for Paywalled Papers](/jordan-gibbs/hyperresearch/how-does-hyperresearch-handle-open-access-recovery)

Discover how Hyperresearch automatically recovers open-access versions of paywalled papers. Learn how it queries Unpaywall, Europe PMC, and CORE to find full-text content.

- Tags: how-to-guide
- Published: 2026-09-13

### [How to Manage Note Status (Evergreen, Stale, Deprecated) in Hyperresearch](/jordan-gibbs/hyperresearch/how-to-manage-note-status-in-hyperresearch)

Master note status management in Hyperresearch. Learn to use evergreen, stale, and deprecated states programmatically or via API for efficient research documentation.

- Tags: how-to-guide
- Published: 2026-09-13

### [How to Synchronize Embeddings in Hyperresearch: CLI and API Guide](/jordan-gibbs/hyperresearch/how-to-synchronize-embeddings-in-hyperresearch)

Learn to synchronize embeddings in Hyperresearch using the CLI and API. Update your research notes' vector representations for fast semantic search with Voyage AI or OpenAI.

- Tags: how-to-guide
- Published: 2026-09-13

### [How Hyperresearch Detects Duplicate Content: Cross-Provider and Note-Level Deduplication](/jordan-gibbs/hyperresearch/how-does-hyperresearch-handle-duplicate-content-detection)

Discover how Hyperresearch detects duplicate content using cross-provider metadata deduplication and note-level shingling. Ensure clean datasets with our advanced approach.

- Tags: how-to-guide
- Published: 2026-09-13

### [Hyperresearch Linting Checks: A Complete Guide to Vault Validation Rules](/jordan-gibbs/hyperresearch/what-kind-of-linting-checks-does-hyperresearch-perform)

Discover Hyperresearch linting checks for validating research vaults. Learn how to ensure structural metadata, provenance, integrity, and compliance with 25+ checks.

- Tags: how-to-guide
- Published: 2026-09-13

### [How to View Individual Notes or Batch Reads in Hyperresearch: A Complete Guide](/jordan-gibbs/hyperresearch/how-to-view-individual-notes-or-batch-reads)

Learn to view individual or batch notes in Hyperresearch with the `hyperresearch note show` command. Choose formatted, raw Markdown, or JSON output for efficient data review.

- Tags: how-to-guide
- Published: 2026-09-13

### [How to Use Semantic Search in Hyperresearch: A Complete Guide to Embedding-Based Retrieval](/jordan-gibbs/hyperresearch/how-to-use-semantic-search-in-hyperresearch)

Unlock semantic search in Hyperresearch with this guide. Learn to generate vector embeddings and enhance retrieval using Reciprocal Rank Fusion for smarter research.

- Tags: how-to-guide
- Published: 2026-09-13

### [How to Perform Full‑Text Search on a Hyperresearch Vault](/jordan-gibbs/hyperresearch/how-to-perform-full-text-search-on-hyperresearch-vault)

Learn to perform full-text search on your Hyperresearch vault. Discover how this powerful tool uses SQLite FTS5 for fast, ranked search via CLI and Python API.

- Tags: how-to-guide
- Published: 2026-09-13

### [Applying Levers to Subagent Prompts in Hyperresearch: A Technical Deep Dive](/jordan-gibbs/hyperresearch/how-are-levers-applied-to-subagent-prompts)

Learn how Hyperresearch applies levers to subagent prompts by rendering runtime instructions into static shim files. Discover how the orchestrator enforces consistent behavior across your research pipeline.

- Tags: deep-dive
- Published: 2026-09-13

### [How to Set Report Voice in Hyperresearch: A Complete Guide to Run Levers](/jordan-gibbs/hyperresearch/what-are-available-levers-for-report-voice)

Master report voice in Hyperresearch by configuring run levers. Learn how the register lever controls narrative tone across four modes with this complete guide.

- Tags: how-to-guide
- Published: 2026-09-13

### [How to Define or Override Research Profiles in Hyperresearch](/jordan-gibbs/hyperresearch/how-to-define-or-override-research-profiles)

Learn to define or override research profiles in Hyperresearch by customizing your config.toml file. Control research depth and agent behavior with simple configuration.

- Tags: how-to-guide
- Published: 2026-09-13

### [How Hyperresearch Persists and Uses the Canonical Research Query](/jordan-gibbs/hyperresearch/how-is-canonical-research-query-persisted-and-used)

Discover how Hyperresearch stores and utilizes the canonical research query in query.md files. Learn how agents, linters, and hooks reference the exact source question for consistent pipeline execution.

- Tags: internals
- Published: 2026-09-13

### [How Hyperresearch Enforces Tool-Locking for Patcher and Polish Auditor Agents](/jordan-gibbs/hyperresearch/how-does-hyperresearch-enforce-tool-locking)

Learn how Hyperresearch enforces tool-locking for Patcher and Polish Auditor agents using YAML definitions and runtime masks. Restrict tools effectively.

- Tags: internals
- Published: 2026-09-13

### [What "Patch, Never Regenerate" Means in Hyperresearch: Immutable Research Outputs](/jordan-gibbs/hyperresearch/what-does-patch-never-regenerate-mean-in-hyperresearch)

Understand the 'patch, never regenerate' concept in Hyperresearch. Learn how this constraint ensures immutable research outputs, preserving provenance and preventing hallucinations for reliable scientific integrity.

- Tags: deep-dive
- Published: 2026-09-13

### [How to Access the Research Vault via the Web UI in Hyperresearch](/jordan-gibbs/hyperresearch/how-to-access-research-vault-via-web-ui)

Easily access your Hyperresearch vault via the web UI. Simply run hyperresearch serve and navigate to the provided URL for seamless data management.

- Tags: how-to-guide
- Published: 2026-09-13

### [How to Access the Research Vault via MCP Server: A Complete Guide](/jordan-gibbs/hyperresearch/how-to-access-research-vault-via-mcp-server)

Learn how to access the research vault via MCP server with this complete guide for jordan-gibbs/hyperresearch. Query, search, and inspect research vaults easily.

- Tags: how-to-guide
- Published: 2026-09-13

### [How the Hyperresearch Research Vault Is Structured: Markdown Layout and SQLite Schema](/jordan-gibbs/hyperresearch/how-is-the-research-vault-structured-in-hyperresearch)

Explore the Hyperresearch vault structure, detailing its markdown layout and SQLite schema. Understand how research data is organized for efficient retrieval and management.

- Tags: internals
- Published: 2026-09-13

### [How Hyperresearch Ensures Adversarial Verification of Citations: A 4‑Layer Defense System](/jordan-gibbs/hyperresearch/how-does-hyperresearch-ensure-adversarial-verification-of-citations)

Discover how Hyperresearch ensures adversarial verification of citations using a 4 layer defense system. Prevent unsupported claims before they enter your report.

- Tags: deep-dive
- Published: 2026-09-13

### [Hyperresearch Pipeline Subagents: Complete Taxonomy of the V8 Agent Architecture](/jordan-gibbs/hyperresearch/what-are-the-different-subagents-used-in-hyperresearch-pipeline)

Explore the Hyperresearch V8 pipeline's sixteen specialized subagents. Learn how fetchers, analysts, critics, and drafters work in parallel to decompose queries, gather evidence, and synthesize reports.

- Tags: deep-dive
- Published: 2026-09-13

### [Understanding the 16-Step Pipeline in Hyperresearch: From Query to Audited Report](/jordan-gibbs/hyperresearch/what-is-the-16-step-pipeline-in-hyperresearch)

Explore the 16-step pipeline in Hyperresearch, a deterministic engine that converts your query into an audited report. Discover how it synthesizes findings for adversarial criticism.

- Tags: deep-dive
- Published: 2026-09-13

### [How to Install and Set Up Hyperresearch: Complete Setup Guide](/jordan-gibbs/hyperresearch/how-to-install-and-set-up-hyperresearch)

Learn how to install and set up Hyperresearch with this complete guide. Quickly install the package, create your vault, and activate the research pipeline for efficient knowledge management.

- Tags: how-to-guide
- Published: 2026-09-13