[Bug] Anthropic API Error 400: System message in messages array breaks session unrecoverably

Bug Description
I'm constantly getting errors like " ⎿  API Error: 400 messages.0: use the top-level 'system' parameter for the initial system prompt" in the midst of a session. There isn't a way to recover from these errors and need to restart work from the start, which is a problem especially if the work wasn't started in plan mode, which means the new session might have a completely different appraoch to the same problem, ruining the reasoning from the earlier session.

Environment Info

• Platform: darwin
• Terminal: iTerm.app
• Version: 2.1.158
• Feedback ID: 220cd8f6-5b25-4bd2-942f-6c279691f1ad

Errors

[{"error":"Error: Tool ToolSearch not found\n    at FOK (/$bunfs/root/src/entrypoints/cli.js:4044:14126)\n    at h3 (/$bunfs/root/src/entrypoints/cli.js:579:21150)\n    at Ww (/$bunfs/root/src/entrypoints/cli.js:579:39921)\n    at s9H (/$bunfs/root/src/entrypoints/cli.js:579:50731)\n    at H7H (/$bunfs/root/src/entrypoints/cli.js:579:87746)\n    at vt (/$bunfs/root/src/entrypoints/cli.js:579:86710)\n    at Nt (/$bunfs/root/src/entrypoints/cli.js:579:86530)\n    at zg (/$bunfs/root/src/entrypoints/cli.js:579:82872)\n    at nH (/$bunfs/root/src/entrypoints/cli.js:579:6559)\n    at UH (/$bunfs/root/src/entrypoints/cli.js:579:5017)","timestamp":"2026-05-30T20:32:36.321Z"},{"error":"Error: Tool ToolSearch not found\n    at FOK (/$bunfs/root/src/entrypoints/cli.js:4044:14126)\n    at h3 (/$bunfs/root/src/entrypoints/cli.js:579:21150)\n    at Ww (/$bunfs/root/src/entrypoints/cli.js:579:39921)\n    at s9H (/$bunfs/root/src/entrypoints/cli.js:579:50731)\n    at H7H (/$bunfs/root/src/entrypoints/cli.js:579:87746)\n    at vt (/$bunfs/root/src/entrypoints/cli.js:579:86710)\n    at Nt (/$bunfs/root/src/entrypoints/cli.js:579:86530)\n    at zg (/$bunfs/root/src/entrypoints/cli.js:579:82872)\n    at j_ (/$bunfs/root/src/entrypoints/cli.js:579:6438)\n    at vM8 (/$bunfs/root/src/entrypoints/cli.js:572:5415)","timestamp":"2026-05-30T20:32:36.344Z"},{"error":"Error: Tool ToolSearch not found\n    at FOK (/$bunfs/root/src/entrypoints/cli.js:4044:14126)\n    at h3 (/$bunfs/root/src/entrypoints/cli.js:579:21150)\n    at Ww (/$bunfs/root/src/entrypoints/cli.js:579:39921)\n    at s9H (/$bunfs/root/src/entrypoints/cli.js:579:50731)\n    at H7H (/$bunfs/root/src/entrypoints/cli.js:579:87746)\n    at vt (/$bunfs/root/src/entrypoints/cli.js:579:86710)\n    at Nt (/$bunfs/root/src/entrypoints/cli.js:579:86530)\n    at zg (/$bunfs/root/src/entrypoints/cli.js:579:82872)\n    at nH (/$bunfs/root/src/entrypoints/cli.js:579:6559)\n    at UH (/$bunfs/root/src/entrypoints/cli.js:579:5017)","timestamp":"2026-05-30T20:32:36.402Z"},{"error":"Error: Tool ToolSearch not found\n    at FOK (/$bunfs/root/src/entrypoints/cli.js:4044:14126)\n    at h3 (/$bunfs/root/src/entrypoints/cli.js:579:21150)\n    at Ww (/$bunfs/root/src/entrypoints/cli.js:579:39921)\n    at s9H (/$bunfs/root/src/entrypoints/cli.js:579:50731)\n    at H7H (/$bunfs/root/src/entrypoints/cli.js:579:87746)\n    at vt (/$bunfs/root/src/entrypoints/cli.js:579:86710)\n    at Nt (/$bunfs/root/src/entrypoints/cli.js:579:86530)\n    at zg (/$bunfs/root/src/entrypoints/cli.js:579:82872)\n    at nH (/$bunfs/root/src/entrypoints/cli.js:579:6559)\n    at UH (/$bunfs/root/src/entrypoints/cli.js:579:5017)","timestamp":"2026-05-30T22:59:22.576Z"},{"error":"Error: Tool ToolSearch not found\n    at FOK (/$bunfs/root/src/entrypoints/cli.js:4044:14126)\n    at h3 (/$bunfs/root/src/entrypoints/cli.js:579:21150)\n    at Ww (/$bunfs/root/src/entrypoints/cli.js:579:39921)\n    at s9H (/$bunfs/root/src/entrypoints/cli.js:579:50731)\n    at H7H (/$bunfs/root/src/entrypoints/cli.js:579:87746)\n    at vt (/$bunfs/root/src/entrypoints/cli.js:579:86710)\n    at Nt (/$bunfs/root/src/entrypoints/cli.js:579:86530)\n    at zg (/$bunfs/root/src/entrypoints/cli.js:579:82872)\n    at nH (/$bunfs/root/src/entrypoints/cli.js:579:6559)\n    at UH (/$bunfs/root/src/entrypoints/cli.js:579:5017)","timestamp":"2026-05-31T01:51:33.767Z"},{"error":"Error: Tool ToolSearch not found\n    at FOK (/$bunfs/root/src/entrypoints/cli.js:4044:14126)\n    at h3 (/$bunfs/root/src/entrypoints/cli.js:579:21150)\n    at Ww (/$bunfs/root/src/entrypoints/cli.js:579:39921)\n    at s9H (/$bunfs/root/src/entrypoints/cli.js:579:50731)\n    at H7H (/$bunfs/root/src/entrypoints/cli.js:579:87746)\n    at vt (/$bunfs/root/src/entrypoints/cli.js:579:86710)\n    at Nt (/$bunfs/root/src/entrypoints/cli.js:579:86530)\n    at zg (/$bunfs/root/src/entrypoints/cli.js:579:82872)\n    at nH (/$bunfs/root/src/entrypoints/cli.js:579:6559)\n    at UH (/$bunfs/root/src/entrypoints/cli.js:57…

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