Runtime: MCP servers not fully loaded on session start and session unrecoverable after interrupt

Start by examining the harness-home canonical projection path for codepilot_runtime, then trace how that runtime discovers MCP servers and handles interrupts. Use the referenced main log and the settings.local.json permissions entry to compare expected and observed behavior. Done means the missing MCP server is loaded and an interrupted session can continue without Tool result is missing errors.

Summary

When using the Codepilot Runtime (codepilot_runtime), two distinct issues are observed:

1. MCP server loading is incomplete: Only a subset of configured MCP servers are synced to the agent loop. The third-party MCP server (codepilot-image-gen) is consistently missing from the tool list, while only playwright and pencil are loaded.

2. Session becomes unrecoverable after interrupt: Interrupting the agent mid-response causes the session to enter a permanently broken state, with Tool result is missing errors persisting across all subsequent turns.

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Environment

• Codepilot version: 0.64.0 (upgraded from 0.63.0 on this session start)
• OS: Windows 11 Pro 10.0.22621
• Runtime mode: codepilot_runtime (pinned in session)
• Project path: C:\Users\Administrator\codepilot

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Issue 1: MCP servers not fully loaded

Observed behavior

Every agent loop turn logs the same line:

[agent-loop] Syncing 2 MCP servers: playwright, pencil

Only 2 MCP servers are synced. The tool list for the agent contains 58 tools total, consisting of built-in tools + Playwright MCP tools + Pencil MCP tools. No tools from the codepilot-image-gen MCP server are present.

Evidence

Log excerpt (repeated across all 7 turns in the session):

[agent-loop] Syncing 2 MCP servers: playwright, pencil
[agent-loop] Session 5857d9d0e7910ef2d8eebd4286c78124: model=deepseek-v4-flash, tools=[Read, Write, Edit, Bash, Glob, Grep, Skill, Agent, codepilot_dashboard_pin, ..., mcp__playwright__*, mcp__pencil__*] (58 total)

The codepilot-image-gen MCP tools are consistently absent from all 58-tool listings across all turns (lines 96, 120, 137, 181, 203, 222, 247, 272, 299, 317 of the log).

Related error

Every turn also logs:

[harness-home] Canonical projection failed { runtimeId: 'codepilot_runtime', reason: 'r is not a function' }

This error occurs on every single request (7 occurrences in the session log). It precedes the tool listing and may be related to the MCP loading failure.

Comparison: Claude Code Runtime works correctly

Under the same working directory, same MCP configuration, and same machine, using the Claude Code CLI Runtime:

• codepilot-image-gen MCP server is loaded automatically on session start
• Agent can directly invoke codepilot_generate_image without any searching or manual configuration
• MCP log confirms successful tool execution: Tool 'codepilot_generate_image' completed successfully in 34s

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Issue 2: Session unrecoverable after interrupt

Observed behavior

When the user interrupts the agent mid-response, the session enters a state where all subsequent turns fail with:

[agent-loop] streamText error: Tool result is missing for tool call call_7718bc899ed247aea103f200.
[agent-loop] Error: No output generated. Check the stream for errors.

Evidence

Interrupt log:

[codex.runtime] interrupt (route) — no active turn for 5857d9d0e7910ef2d8eebd4286c78124
[interrupt] fan-out { sessionId: '5857d9d0...', attempted: { native: true, codex_runtime: true, sdk: false } }

After the interrupt, the user sent 6 more messages. All of them failed with the same Tool result is missing error. Even switching the model (from deepseek-v4-flash to doubao-seed-2.1-turbo to claude-sonnet-5) and provider did not recover the session. The error persisted across model changes, and the sdk_session_id was repeatedly cleared and reset.

The session eventually became so broken that the user had to open a new session (478f123a...), but even that new session showed the same MCP loading issue (only 2 MCP servers synced).

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Root cause analysis (speculative)

The recurring [harness-home] Canonical projection failed { runtimeId: 'codepilot_runtime', reason: 'r is not a function' } error suggests:

1. The harness-home module (likely responsible for resolving the home directory / config path for the agent harness) is failing during canonical projection — a path normalization operation
2. The error 'r is not a function' indicates a JavaScript runtime error, possibly a function reference that was expected but not found (e.g., a callback, a method on a config object, or a module export)
3. This failure may prevent the MCP configuration from being fully discovered and loaded, since MCP server definitions typically reside in the home directory config

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Suggested investigation areas

1. harness-home module: Examine the canonical projection function for the runtimeId: 'codepilot_runtime' code path. The 'r is not a function' error suggests a variable r is expected to be a function but is undefined or of a different type.

2. MCP server discovery: Compare how the Codepilot Runtime discovers MCP servers vs. the Claude Code Runtime. The Codepilot Runtime may be using a different config resolution strategy that doesn't pick up all MCP servers.

3. Interrupt recovery: The interrupt handler attempts recovery via native and codex_runtime but neither succeeds. The Tool result is missing error suggests the interrupt left the tool call state machine in an inconsistent state.

4. MCP server definition location: The codepilot-image-gen MCP server is only referenced in the project's settings.local.json permissions list. Its mcpServers definition may be in a non-standard location that the Codepilot Runtime doesn't check.

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Configuration files

Project settings.local.json:

{
  "permissions": {
    "allow": [
      "mcp__codepilot-image-gen__codepilot_generate_image"
    ]
  }
}

Global ~/.claude/settings.json: Contains env vars, plugin config, theme, and permissions — but no mcpServers section relevant to codepilot-image-gen.

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Log reference

• Session ID: 5857d9d0e7910ef2d8eebd4286c78124 (broken session)
• Log file: %APPDATA%\codepilot\logs\codepilot-main.log
• MCP log (working): %LOCALAPPDATA%\claude-cli-nodejs\Cache\C--Users-Administrator-codepilot\mcp-logs-codepilot-image-gen\2026-08-03T05-34-03-041Z.jsonl