Problem

Workspace bootstrap files (AGENTS.md, SOUL.md, TOOLS.md, IDENTITY.md, USER.md, HEARTBEAT.md, MEMORY.md) are injected into every agent run regardless of session type. This wastes tokens:

• DM sessions load HEARTBEAT.md (~300-1,500 tokens) which contains heartbeat poller instructions not needed during interactive conversations
• Heartbeat runs load SOUL.md, TOOLS.md, USER.md, MEMORY.md which are not needed for a periodic check

For users with multiple agents and detailed HEARTBEAT.md files, this adds up to 1,400+ wasted tokens per DM message.

Solution

Extend filterBootstrapFilesForSession() to support session-type-aware filtering:

• Subagent sessions: AGENTS.md + TOOLS.md (unchanged, existing behavior)
• Heartbeat sessions: HEARTBEAT.md + AGENTS.md + IDENTITY.md (new)
• Normal DM sessions: All files except HEARTBEAT.md (new)

The isHeartbeat flag is threaded from the auto-reply layer through the embedded runner to the bootstrap file resolver.

Changes

• workspace.ts: Added HEARTBEAT_BOOTSTRAP_ALLOWLIST, DM_BOOTSTRAP_EXCLUDELIST, and FilterBootstrapOptions type. Extended filterBootstrapFilesForSession() with optional opts parameter.
• bootstrap-files.ts: Thread isHeartbeat through resolveBootstrapFilesForRun and resolveBootstrapContextForRun.
• run/types.ts + run/params.ts: Added isHeartbeat? to embedded run params.
• run/attempt.ts + run.ts: Pass isHeartbeat to bootstrap context resolver.
• followup-runner.ts + agent-runner-execution.ts: Pass isHeartbeat to embedded runner.

Testing

• All existing tests pass (workspace.test.ts: 4/4, bootstrap-files.test.ts: 2/2)
• Backward compatible: the opts parameter is optional, existing behavior unchanged when not provided

Related Issues

• Performance: Workspace file injection wastes 93.5% of token budget #9157 (workspace file injection wastes 93.5% of token budget)
• the tokens got burned by dragging a huge context forward #1594 (heartbeat cron jobs load full main session context)

Greptile Overview

Greptile Summary

This PR adds session-type-aware bootstrap file filtering to reduce token waste: subagent runs continue to load a minimal allowlist, heartbeat runs load only HEARTBEAT.md + core identity/agent files, and normal DM sessions load everything except HEARTBEAT.md. The new isHeartbeat flag is threaded from the auto-reply layer through the embedded runner into the bootstrap resolver, which then calls the updated filterBootstrapFilesForSession().

Main issue to address before merge: followup runs don’t register isHeartbeat in the agent run context, which can break downstream behavior that relies on getAgentRunContext(runId)?.isHeartbeat (notably webchat broadcast suppression for heartbeats).

Confidence Score: 3/5

• Not safe to merge until followup heartbeat runs are correctly classified.
• The bootstrap filtering and isHeartbeat threading are mostly consistent, but followup runs omit isHeartbeat when registering AgentRunContext, which breaks downstream heartbeat-specific behavior (e.g., suppressing heartbeat broadcasts).
• src/auto-reply/reply/followup-runner.ts

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