PaperClipAI/doc/connections/GITHUB.md

GitHub managed connection

GitHub is a Paperclip Cloud-managed GitHub App connection with an advanced PAT compatibility method. Cloud owns the fixed public OAuth callback and signed webhook inbox; provider tokens are sealed to the enrolled instance and stored only in its existing encrypted secret system.

Catalog entries

GitHub connects an account for repository tools, Git, and gh, and opens Access → Connect directly. GitHub Code Review Bot connects one agent to a GitHub App for pull-request reviews and mentions, and opens Choose agent directly. The bot entry follows Settings → Experimental → GitHub review bots (enableGitHubReviewBots), which defaults to off. It is independent of Chat connectors: enabling one does not enable the other. Turning off the GitHub setting hides setup and management; existing bots keep running.

Both entries reuse the existing GitHub integrations. Bot endpoints retain the github provider identity and existing setup, reconnect, and management URLs; saved bot connections and drafts appear under GitHub Code Review Bot. GitHub repository and MCP URLs still resolve to the ordinary GitHub tool connection.

Bot instructions and triggers

Bot Settings uses the shared Markdown editor for common and event-specific instructions. Type / and select a company skill to insert a saved skill link. Common instructions accompany every admitted GitHub task; event-specific instructions accompany that event. Selected skills are materialized for the run and explicitly invoked by the native Runner, subject to existing tool and isolation restrictions. The admitted configuration snapshot determines skill selection for each wake, including queued events. GitHub messages, repository content and other companies' skills cannot assign skills to the run.

Authorized @mentions remain available when Run automatically is on or off. The switch in Settings reveals the PR and issue event checkboxes. Access lists company members and external contributors separately. Author include/exclude filters in Settings control whose activity starts automatic work; there is no per-person automatic-run switch. Automatic events still require an authorized author and an enabled event. Legacy people[].automaticReviews values are accepted but ignored. External contributors additionally need Allow automatic runs for external contributors. Their restricted guest profile and sponsor requirements are unchanged.

The passing-score number field accepts a whole number from 1 to 5, defaulting to 5. Paperclip publishes a successful Paperclip Review check only after a complete assessment of the current commit meets the threshold; lower scores fail and incomplete assessments require action. To block merging, separately require this check from the dedicated App in GitHub branch protection or a ruleset. A new head commit needs its own check. Report-only mode publishes a neutral conclusion, which GitHub can accept for a required check; it does not enforce a score requirement. This includes incomplete assessments and failed runs: their checks remain neutral and explain the failure without presenting a passing assessment. A passing score does not formally approve a PR. Approvals and change requests contains those optional agent permissions. Scheduling filters, ignored files, and inline-comment options have separate disclosures. The header shows the App identity, copyable mention, avatar download, and GitHub branding settings.

Published review summaries use the GitHub bot's display name in their heading. The check name remains Paperclip Review. Multiple bots can review the same PR through separate GitHub Apps: each keeps its own task, summary, findings, and check. Check updates match both the App ID and the endpoint/PR/commit identity. Repository branch rules decide separately which App's check is required to merge.

Self-hosted setup

The setup screen states the default access in one line, with Change for other choices. Continue to GitHub on that screen starts the provider handoff.

A self-hosted instance needs one Paperclip Cloud approval before its first managed connection. After approval, setup returns to the connect screen and continues to GitHub without another instance approval or a service restart.

If an unapproved enrollment link expires, return to setup and select Continue. Paperclip asks the server for a valid link. The server reuses a live pending enrollment or replaces an expired one; this does not revoke or repeat an existing instance approval.

Identity resolution

Every MCP call, gh invocation, native Git operation, checkout, health check, and webhook binding uses the same order:

1. An active dedicated GitHub grant for the current agent.
2. The active personal GitHub grant owned by the run's responsibleUserId.
3. For automated work without a responsible user, a personal grant only when an existing standing delegation names the agent.
4. Legacy GH_TOKEN/GITHUB_TOKEN only when no managed GitHub connection is configured for the company.

An unavailable or ambiguous managed identity fails visibly. It never falls through to another person, an organization credential, or a legacy token. Agent grants are company-scoped, have exactly one subjectAgentId, cannot be organization defaults, and are installed only for that agent.

The connection installation is the credential owner's consent boundary. A personal setup may target every agent or a selected set, and runtime resolution considers only an enabled, active connection installed for the current agent. Within that boundary, Paperclip treats the run's server-resolved responsibleUserId as its credential principal, including for automated work; agents cannot choose or spoof this field. The owner must still be an active non-viewer company member at each use. A standing delegation is needed only when a run genuinely has no responsible user.

Credential lifecycle

The production, staging, and development GitHub Apps deliberately disable user-to-server token expiration. The resulting long-lived access token is checked with GitHub's /user endpoint every 30 days, together with installation and repository summary refresh. Routine continuity requires no browser visit.

If GitHub returns an expiring access token and rotating refresh token instead, Paperclip stores both encrypted and:

• refreshes at least one hour before access expiry;
• forces a rotation at least every 30 days while the instance is active;
• serializes refresh through the existing database refresh lease and compare- and-swap update;
• atomically advances both secret values before clearing the lease;
• retries one forced refresh after a provider 401.

Only an unrecoverable provider invalidation marks a grant needs_reauthorization. Installation removal or suspension is reported as an installation-health failure, not as token expiry.

Repository access

OAuth completion verifies /user, every page of /user/installations, and every page of each installation's accessible repositories. Setup remains incomplete until at least one installation and repository are available. Paperclip stores the authenticated username and a grant-scoped display snapshot containing only repository IDs, full names, installation IDs, and private-repository flags. GitHub stays authoritative: this snapshot never authorizes repository access.

The permissions page shows repositories across authorized accounts by default. Use the account filter and search to narrow the list. The list scrolls after about ten rows and marks known private repositories with a lock. Configure on GitHub opens the app account chooser so users can add or update organization access. Refresh access after changing the selection. Older snapshots omit the private flag until refreshed. If a legacy grant lacks its app chooser URL, Load GitHub configuration refreshes access and recovers the app slug from GitHub installation metadata. The page does not substitute a single-installation settings URL for the account chooser.

The permissions page shows the authenticated GitHub account and the complete accessible repository list. Refresh access reloads it from GitHub. Older grants and grants invalidated by newer installation lifecycle events prompt for a refresh instead of presenting a stale list. The page links to GitHub's installation management page. Selected repositories are recommended; all- repository access retains its warning.

Fresh local test-drives use production Paperclip Cloud. Instance enrollment and provider enablement are separate: enrollment alone does not enable GitHub OAuth. Production must advertise the github.code profile (see Cloud's docs/github-connector-deploy-bootstrap.md). If it is unavailable, setup preserves the sign-in intent and offers a retry instead of silently switching to a personal access token. A successful retry preserves the chosen audience.

GitHub Actions tools

Managed and PAT connections request X-MCP-Toolsets: default,actions for MCP discovery and invocation. GitHub's default catalog excludes Actions; granting Actions permissions alone does not expose workflow tools. Existing connections can use Refresh actions after upgrading to discover the added tools. The normal catalog, access, approval, and quarantine rules still apply.

To dispatch an existing workflow, use actions_run_trigger with method: "run_workflow", the repository owner and name, workflow_id, ref, and any workflow inputs. The workflow must declare workflow_dispatch. The GitHub App installation or fine-grained PAT needs Actions: Read and write for the repository. App owners set that permission on the GitHub App registration; installation owners must approve an increase before it takes effect. Paperclip's action controls do not grant GitHub permissions.

The tool also supports rerunning and cancelling runs and deleting run logs. It retains GitHub's destructive classification. Read tools include actions_list, actions_get, and get_job_logs.

Provider references: MCP toolset configuration and workflow dispatch permissions.

Webhooks

For the shared GitHub account connector, Paperclip Cloud verifies X-Hub-Signature-256 against the exact bounded request body before parsing, deduplicates by X-GitHub-Delivery, and persists a minimal normalized event before returning 202. Raw webhook payloads are discarded. When registering an active binding, Paperclip sends the current user token only inside the signed, payload-bound broker request so Cloud can verify access to that exact installation; Cloud neither logs nor persists that proof token. Deliveries fan out independently to every enrolled instance bound to the GitHub installation and are sealed to each instance's public key.

The instance polls with backoff, stores a company-scoped idempotency receipt, and acknowledges only successful applications. A merged pull request updates its matching external-object snapshot and immediately runs the existing merge- confirmation resolver. It wakes the assignee only when that interaction's continuation policy requests it; unrelated Paperclip issues are not closed. The periodic GitHub merge sweep remains the reconciliation fallback.

Installation lifecycle events refresh or invalidate installation summaries and remove obsolete Cloud bindings. Activity records contain event identifiers and outcomes but no webhook content. GitHub webhook content is never first-party telemetry.

Dedicated agent Apps

The bot wizard uses Cloud gateway protocol version 2. The stack builds the private manifest for a personal account or organization. GitHub still asks the user to confirm creation and repository installation. The stack exchanges the returned manifest code directly with GitHub and stores every App secret in its vault, including the private key, client secret, and webhook verifier.

Cloud stores only opaque, instance-bound callback routes and encrypted callback claims. It does not exchange codes, track App or installation identity, store GitHub secrets, or interpret bot events. It forwards original webhook bytes, provider headers, and signature in an envelope sealed to the stack before writing the inbox. The stack decrypts and authenticates those bytes through its existing durable ingress. Cloud-managed Apps are excluded from the direct-tenant callback recovery scanner and its callback-mismatch warning; the Cloud inbox owns relay delivery retries. Only that local check can verify a connection or admit work. After a repair, a fresh authenticated event for the bound installation can verify webhook delivery even when the relay deduplicates a redelivered old ping. This also applies while the connection needs attention: the signed event verifies delivery without retaining its content, admitting work, or changing repository access, even when its repository is disabled or unavailable. Verification returns the connection to the provider-setup step; later installation events cannot activate it. The manager must still complete reconnect and activation before new review requests can run. Shared-App account connectors keep the behavior described above.

Unverified gateway traffic has request, byte, pending-queue, retention and wake limits. Its transport deduplication includes the body and signature, so a forged request cannot occupy a real delivery's identifier. A ping received before its verifier reaches the vault remains queued for retry. Malformed and forged traffic is discarded after local verification. Installation returns only request a state refresh; the stack queries GitHub to establish installation authority.

OAuth state, PKCE, consent, repository discovery, recovery and lifecycle changes also stay in the stack. Interrupted single-use manifest exchanges require recovery of the existing App instead of a second creation. Direct webhook and manual existing-App recovery remain available. Connecting does not prove that an agent runtime can execute a review.

One main response per pull request

A pull request task can retain both its main discussion and inline finding threads. Bot tool discovery lists each endpoint/catalog tool once across those threads. Publishing an inline finding therefore does not duplicate the tool catalog on the task's next run. Both conversation mappings remain available for authorized follow-up replies.

The main PR conversation shares one App-owned comment across pushes, mentions, and repeat reviews. A new request updates that comment to Review queued…; agent progress and the final assessment update the same comment. Its identity survives restarts and reconnects. Existing request comments can be adopted without creating another main comment. Issue conversations and inline-review threads retain one editable response per request. Description mentions and automatic tasks also receive an acknowledgement. No new eyes reaction is added; cleanup still handles receipts created by older versions.

The agent's update_comment tool edits the current request's working comment. It takes a body and a stable idempotency key, with no caller-selected comment ID or destination. Instructions encourage brief, factual progress updates during longer work. Distinct updates use distinct keys; retries reuse the same key. Progress does not complete an assessment or change a review check.

The comment tool replaces that same comment with the final answer. submit_review replaces it with the allowed review summary; checks, inline findings and explicitly permitted formal reviews remain separate. Corrected assessments can update the summary again. Delayed progress cannot overwrite a final answer. Native final text stays in Paperclip and creates no extra comment. Legacy connections without a saved review configuration retain automatic run progress and final replies until upgraded to this tool-owned response model.

Receipts are bound to the company, App, task, accepted request and original runtime generation. The existing publication lease serializes edits, and App-owned markers recover uncertain creation without posting duplicates. Deleted or no-longer-owned comments are not recreated or edited. Coalesced runs settle a deleted earlier working comment without blocking the current response, review findings, or check publication. Failed runs update the same comment when no final reply is confirmed or unresolved. Maintenance also reconciles acknowledged requests when recovery stops before a publication is staged. Requests saved on a blocked task report that work is paused and stay open for resumed progress or stopped-run cleanup. An older run cannot replace a newer run's response. A run that ends without a final reply clears a remaining working state honestly. Repository restrictions, person authorization and governed tool checks remain in effect for edits. Existing disabled or quarantined tools stay disabled. Existing native sessions refresh incompatible tool checkpoints so the agent can see update_comment. The same Paperclip task and saved history remain.

Explicit bot mentions and subscriptions

Issue and PR descriptions, discussion comments, inline comments, and review summaries retain uploaded attachment references when they mention the bot. Private images use the exact unchanged source's authenticated GitHub rendering; repository/thread identity and body hashes remain bound across restarts. Signed image URLs and credentials are never added to durable attachment descriptors.

A manual message beginning with another recipient's @mention does not wake this bot through its thread subscription, including Apps outside Paperclip such as @greptile review. Mentions of other connected GitHub bots are also filtered elsewhere in the body. Paperclip filters that delivery before creating task work or adding an acknowledgement. Explicitly mentioning both bots allows both to receive the request, subject to their normal authorization and repository checks.

Unaddressed follow-ups and incidental human or unknown mentions retain the existing subscription behavior. Explicitly mentioning this bot admits a request even when another recipient is named. The routing rule does not change automatic issue or PR event policies. Archived bots and identities from other companies or providers are excluded from the routing lookup.

Run projection

The resolved token is leased at run start as an audited class-3 secret and is projected only into the child process:

• GH_TOKEN, GITHUB_TOKEN, and an internal credential-helper environment key;
• GIT_TERMINAL_PROMPT=0;
• process-scoped GIT_CONFIG_COUNT/KEY_n/VALUE_n entries that clear ambient helpers, install a github.com-only helper, and rewrite GitHub SSH remotes to HTTPS;
• author and committer identity using <numeric-id>+<login>@users.noreply.github.com.

Tokens never appear in arguments, URLs, files, logs, events, or model context, and the projection never replaces HOME.

Cloud deployment and exact GitHub App registration settings live in paperclip-cloud/docs/github-connector-deploy-bootstrap.md.