fix(agent): preserve uploaded project files

[iamjr15]

Why

Uploaded project files must remain durable user-owned inputs even when an agent, scaffold, repository import, failed run, or stale sandbox mutates the workspace cache. R2 remains the authoritative immutable store.

What changed

• restore missing, replaced, or modified uploaded files from checksum-verified R2 versions before every project-bound run and again during cleanup
• make the workspace upload cache read-only and reject upload mutations through file write/delete tools
• preserve uploads/ during template resets and repository imports
• instruct the agent to copy uploads elsewhere before transforming them
• make runtime-manifest publication tolerate toolbox/container mount visibility lag
• document the ownership and repair contract

Verification

• pnpm turbo lint typecheck build — 76/76 tasks passed
• affected-package Biome, dependency-cruiser, and Knip checks passed
• exact single migration packages/db/drizzle/0000_current_schema.sql dry-ran against production and verified the schema contract
• pnpm dev built and started the complete local Compose stack on Node 24.18.0
• direct local browser QA rendered the authenticated app, and gateway/agent/webhooks health checks were healthy
• no database schema change; the repository still has exactly one migration file

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1 Skipped Deployment

Project	Deployment	Actions	Updated (UTC)
cheatcode	Skipped		Jul 27, 2026 2:37pm