fix(cli): make repeated --messages last-flag-wins (#416)

`--messages -` set messagesFromStdin, and a later `--messages <file>` set
messagesJSON without clearing that flag. The result carried both, and main.swift
checks messagesFromStdin first, so the file that had already been read,
validated and parsed was thrown away and stdin was used instead.

Every other repeated flag in this parser is last-wins, so this one silently
disagreed. The practical case is a wrapper script or alias that already passes
`--messages -` and a user who appends `--messages conversation.json`: apfel read
empty stdin, reported "invalid --messages JSON from stdin" and exited 2 while a
perfectly good conversation file sat unused -- with the error pointing at a
source the user never asked for on that invocation, which is what made it hard
to diagnose.

Each branch now resets the other.

Verified red-to-green: with the two reset lines removed, the two ordering tests
fail (the file case reports messagesFromStdin still true, the stdin case reports
messagesJSON still populated); with them, 1078 tests pass. Confirmed live too --
`--messages file --messages -` now answers from stdin.

Diff taken from candidate PR #421.

Closes #416

Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_011ccLBbEaVVd4sJyUd5wyhA