refactor: serialize --apply and --contain from flags

[SebTardif]

Summary

Build Patchloom argv from structured flags instead of scanning a flat string[] for --apply and --contain.

Why

PR #254 stopped Array.includes from treating user text as a flag. That was still argv surgery: helpers looked at token slots in the same array that holds replace/search text.

The extension is not a CLI parser. It should not search operands for option names.

The change

• PatchloomInvocation carries args, apply, and contain.
• serializePatchloomArgs prefixes --contain and appends --apply from those booleans only.
• Builders that write (create, undo, patch apply, patch merge) set apply: true and no longer put --apply in args.
• executePatchloom serializes at execFile.
• Batch Apply uses the same serializer.

This does not add commander/yargs. It also does not change how clap sees a positional that looks like a flag (for example replace old text --apply). That would need a named operand on the CLI.

Verification

• npm run check passed (429 unit tests, 7 skipped, coverage, package).

Checklist

• All commits in this pull request are signed off with git commit -s
• I ran npm run check and it passes
• I updated docs if user-facing behavior changed
• I am contributing this work under the repository license (MIT)