effect(patch,tool): migrate patch/index and tool/read to AppFileSystem

[kitlangton]

Summary

• src/patch/index.ts: the apply path now returns Effect<...> values backed by AppFileSystem.Service. The pure parser, chunk replacer, and shell-argv parser stay sync. deriveNewContentsFromChunks is now a pure function that takes the original file text as an argument — callers (apply_patch tool and applyHunksToFiles) supply the content they already have, removing the embedded readFileSync.
• src/tool/apply_patch.ts: passes the already-read source text to deriveNewContentsFromChunks instead of letting the parser do its own filesystem read.
• src/tool/read.ts: drops fs.createReadStream + readline in favor of a Stream pipeline over AppFileSystem.Service.stream. Offset / limit / byte-cap behavior is preserved.

Shape change in patch/index.ts

• applyHunksToFiles, applyPatch, and maybeParseApplyPatchVerified are now Effect.fn(...) values returning Effect<...>; they require AppFileSystem.Service.
• deriveNewContentsFromChunks(filePath, chunks, originalText) now accepts the original text and is fully pure (no fs I/O).
• The parser surface (parsePatch, maybeParseApplyPatch) is unchanged.

Line-streaming behavior in tool/read.ts

• Uses AppFileSystem.Service.stream + a manual TextDecoder ({ stream: true }) + Stream.splitLines + Stream.runForEach.
• The manual decoder is intentional: Stream.decodeText drops the final unterminated line when the source ends without a flush, and Stream.runForEachWhile drops the last splitLines chunk. The done flag in the callback replaces the original break for the byte-cap path so line counting matches the previous semantics.
• Offset / limit / MAX_LINE_LENGTH truncation / MAX_BYTES cut / more / cut flags all match the previous helper.

Refs

• packages/opencode/specs/effect/tools.md — read.ts and patch/index.ts cleanups marked done.

Test plan

• bun run typecheck
• bun run test test/patch/patch.test.ts (20 pass)
• bun run test test/tool/apply_patch.test.ts (27 pass)
• bun run test test/tool/read.test.ts (39 pass)
• bun run test — 2574 pass, 0 fail