feat: add fast existing-file edits and resilient previews

[iamjr15]

Summary

• Show Working immediately after submission while preserving a single continuous elapsed timer into the real response.
• Replace timestamp-based Daytona source sync with content-addressed, atomic, crash-safe synchronization and package transactions.
• Add production Morph FastApply support for existing UTF-8 files through a bounded REST client and conflict-safe sandbox writes.

What's Included

Immediate run feedback

• Adds a view-only pending assistant state before the first streamed response.
• Prevents duplicate pending states during reconnects and keeps elapsed time stable.

Resilient sandbox synchronization

• Uses SHA-256 content identity instead of comparing clocks across filesystems.
• Makes file replacement atomic and handles file, directory, and symlink type changes.
• Uses an OS lock and a three-way, conflict-aware package transaction that releases automatically after crashes.

Production FastApply

• Adds a small first-party Morph REST package with strict validation, bounded bodies, timeouts, and transient retries.
• Resolves the Morph credential lazily from Cloudflare Secrets Store inside the active run.
• Adds fs_apply for existing text files and preserves fs_write for creation, binary data, and full replacements.
• Commits generated edits with a compare-and-swap write so concurrent source changes cannot be overwritten.

Architecture

The agent reads an existing file from the sandbox, sends the original content plus a sparse edit to Morph, and commits the generated candidate only when the source hash still matches. Daytona local package execution now performs force-sync, command execution, and conflict-aware commit under one process lock. The web client renders submission feedback locally until the authoritative stream arrives.

Decisions Made

Decision	Choice	Alternatives considered	Reasoning
Morph integration	Bounded first-party REST client	Pre-1.0 SDK	Keeps the Worker dependency surface small and makes limits, validation, retries, and error redaction explicit.
Existing-file writes	Compare-and-swap	Unconditional overwrite	Prevents stale model output from clobbering concurrent edits.
Source identity	SHA-256 content hashes	Cross-filesystem mtimes	Clocks and timestamp granularity differ across Daytona object storage and native disk.
Package transaction	One locked remote operation	Prepare/commit/abort markers	OS locks are released on process death and eliminate stale marker recovery.
Pending UI	View-only synthetic assistant	Persisted placeholder message	Gives immediate feedback without corrupting durable chat history.

Edge Cases Handled

Scenario	Handling
Equal-size edit with older mtime	Content hashing still detects it.
Process crash during package command	OS lock releases and durable source remains unchanged.
Concurrent file edit during FastApply	Hash mismatch returns a retriable conflict.
Provider redirect or oversized response	Request is rejected at the client boundary.
Reconnect with an existing assistant response	Pending UI is not duplicated.

Verification

• pnpm lint
• pnpm typecheck
• pnpm turbo build --force
• pnpm deadcode
• pnpm architecture:check
• pnpm turbo skills:build
• Deterministic synchronizer harness: content, deletion, retyping, transaction, conflict, and crash cases
• Production Worker dry-run with the Morph Secrets Store binding
• Production browser QA after merge and snapshot promotion