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GitHub is where your team’s engineering decisions are made — in pull request reviews, issue discussions, and the markdown documentation living alongside your code. When you connect GitHub to Hyper, it indexes PRs, issues, and markdown files across your selected repositories, giving AI agents rich context about what your team has built, debated, and decided. Hyper supports multiple GitHub accounts and lets you choose which repositories to sync, keeping your memory layer focused on the projects that matter.

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Connect GitHub

1

Open Settings in the Hyper desktop app

Launch the Hyper desktop app and click Settings in the navigation, then select Connections.
2

Click Connect next to GitHub

Find GitHub in the list of available integrations and click Connect.
3

Install the Hyper GitHub App

You’ll be directed to authorize the Hyper GitHub App on your GitHub account. This is a GitHub App installation — not a personal access token. Using a GitHub App gives Hyper precisely scoped access and is the secure, recommended approach for team use.
4

Select repositories to sync

During the GitHub App installation, choose which repositories Hyper can access — either all repositories on your account or a specific subset. You can update this selection later from your GitHub App settings.
5

Wait for the initial sync to complete

Hyper begins indexing PRs, issues, and markdown files from your selected repositories. Sync progress is visible in Settings → Connections.
6

Add more GitHub accounts (optional)

To connect additional GitHub accounts (for example, a personal account alongside an organization account), return to Settings → Connections and click Connect next to GitHub again.
Hyper uses a GitHub App installation rather than a personal access token. GitHub Apps have granular, auditable permission scopes and can be installed at the organization level — making them suitable for team-wide deployments.

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What Hyper Syncs

What’s syncedDetails
Pull requestsTitle, description, comments, review discussions, and state
IssuesTitle, body, comments, labels, and state
Markdown filesAll .md and .mdx files in the repository tree
Incremental updatesNew commits trigger re-sync via commit comparison — only changed files are re-indexed
Multi-repoYou select which repositories to sync at install time
Multiple accountsEach GitHub account is a separate connection
Source linksEach item links back to https://github.com/{owner}/{repo}/blob/main/{path}
Hyper reads repository content only — it never creates, edits, or closes PRs, issues, or files on your behalf.

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Search GitHub with AI Agents

Once your repositories are indexed, your AI agents can search PRs, issues, and markdown files using powerful filters or natural language. Supported search filters:
FilterExampleWhat it does
author:author:aliceItems created by a specific user
state:state:openFilter by open or closed state
is:pris:prPull requests only
is:issueis:issueIssues only
is:mergedis:mergedMerged pull requests
is:draftis:draftDraft pull requests
Example agent queries: 
Find open PRs by alice related to authentication
Search GitHub issues about database connection timeouts
Show me merged PRs in the api-service repo from last sprint
Find draft PRs in the frontend repo
Read PR #342 in owner/repo
Search markdown files mentioning "rate limiting" across all repos
Find closed issues labeled "bug" authored by bob
What agents can do:
ActionDescription
Search PRsQuery pull requests with state, author, and type filters
Search issuesQuery issues with status, author, and label filters
Search markdownFull-text search across all indexed .md and .mdx files
Read by referenceFetch a specific PR, issue, or file using owner/repo#number or a file path
For repositories with many files, Hyper performs an initial full crawl and then switches to incremental updates based on commit comparisons. Only files changed in new commits are re-indexed, keeping sync fast regardless of repository size.

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Reconnect GitHub

If the GitHub App installation is suspended or revoked, Hyper will display a Reconnect prompt in Settings → Connections.
1

Go to Settings → Connections

Open the Hyper desktop app and navigate to Settings → Connections.
2

Click Reconnect next to the affected GitHub account

Each GitHub account has its own connection entry. Click Reconnect for the one that needs re-authorization.
3

Re-install or re-authorize the GitHub App

Follow the GitHub App authorization flow. Your previously indexed data is preserved — Hyper resumes sync from the latest commit.

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Disconnect GitHub

To remove a GitHub account from Hyper, go to Settings → Connections, find the GitHub entry, and click Disconnect. To fully revoke access, also uninstall the Hyper GitHub App from your GitHub account’s settings page.
Disconnecting GitHub removes all indexed PR, issue, and markdown data for that account from Hyper’s memory layer. Other connected GitHub accounts are unaffected.