fix(cli): exclude scoped instructions from SWE-Pruner

[marius-kilocode]

Directory-scoped AGENTS.md files are appended to read output before SWE-Pruner runs. Successful pruning could remove those instructions while preserving metadata that prevents them from being attached again, leaving the main agent without applicable rules.\n\nThis change separates generated instruction reminders from the prunable file body, sends only source content to the skimmer, and restores the reminders byte-for-byte afterward. Inconsistent reminder metadata fails open to the original output, while pruning metrics continue to account for every line returned to the main agent.

[kilo-code-bot]

Code Review Summary

Status: No Issues Found | Recommendation: Merge

Reviewed the partition() split logic against read.ts's output construction (file vs. directory branches, image/PDF branch, metadata.loaded semantics, and the includeDirectoryFiles expand path) and confirmed the body/tail split is sound: the <system-reminder> block is only ever emitted once, after </content>, and only on the single-file read path that also sets metadata.loaded. The line-numbered content construction makes the marker strings unreachable inside real file content, so the new indexOf-based partitioning won't misfire. The added test exercises the real SwePruner.sweep Effect (via Effect.provideService, not internal mocks) and verifies the skimmer never sees the appended instructions, including a CRLF line-ending edge case. Changeset is present and accurately describes the user-facing behavior. All changes are confined to packages/opencode/src/kilocode/ and packages/opencode/test/kilocode/, so no fork-hygiene concerns.

Files Reviewed (3 files)

• .changeset/protect-swe-pruner-instructions.md
• packages/opencode/src/kilocode/swe-pruner.ts
• packages/opencode/test/kilocode/swe-pruner.test.ts

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_{Reviewed by claude-sonnet-5 · Input: 40 · Output: 16.3K · Cached: 1.2M}

_{Review guidance: REVIEW.md from base branch main}