fix(core): preserve UTF-8 BOM in filesystem writes

[noobezlol]

Fixes #11901

Summary

• Wrap AppFileSystem.readFileString so UTF-8 BOM-prefixed files return the BOM marker that Effect's TextDecoder strips by default.
• Wrap AppFileSystem.writeFileString so overwriting an existing BOM-prefixed file preserves the marker unless the write is an append-style operation.
• Route readJson, writeJson, and string writeWithDirs through the BOM-aware helpers while keeping JSON parsing free of the marker.
• Add focused regression coverage for reading, direct overwrites, edit-style writeWithDirs, and JSON read/write behavior.

Tests run

• bunx prettier --check packages/core/src/filesystem.ts packages/core/test/filesystem/filesystem-bom.test.ts (from repo root) - passed.
• bun run lint packages/core/src/filesystem.ts packages/core/test/filesystem/filesystem-bom.test.ts (from repo root) - passed: 0 warnings, 0 errors.
• bun test test/filesystem/filesystem-bom.test.ts (from packages/core) - passed: 4 pass, 0 fail.
• bun test test/filesystem/filesystem.test.ts (from packages/core) - passed: 26 pass, 0 fail.
• bun run typecheck (from packages/core) - passed.
• git diff --check - passed.

Notes

• The issue referenced the older packages/shared/src/filesystem.ts path; on current main, this shared filesystem service lives at packages/core/src/filesystem.ts.
• To run the checks in this sparse D-drive checkout, I populated missing workspace packages with git sparse-checkout add packages/kilo-sandbox, git sparse-checkout add packages/kilo-gateway, and git sparse-checkout add packages/sdk/js. Git emitted Windows long-path warnings while scanning nested node_modules, but the commands completed.

Risk / compatibility

• Low risk for normal UTF-8 files: files without an existing BOM continue to write without one.
• Existing BOM-prefixed files keep their marker across string overwrites and JSON writes.