Three issues from an adversarial review, all rooted in the startup argv parse
running before extensions load:
1. Flag-looking string values (`--name --print`): the extension-aware reparse
consumed the following token as the value, disagreeing with the startup
parse that treated `--print` as the built-in flag — so the reparse could
silently flip command shape. Extension string flags now consume a following
token only in `--flag=value` form or when it is not flag-looking; pass a
flag-looking value as `--flag=value`. Keeps both parses consistent.
2. `@file` string values (`--target @notes.md`): file args were processed from
the startup parse, which misreads the value as a file and reads it into the
prompt. processFileArguments now runs on the extension-aware parse
(initialArgs.fileArgs); pipedInput stays early for mode detection.
3. Built-in collisions: an extension flag named like a built-in (e.g. `model`)
was consumed by the built-in branch and never delivered to the runner.
registerFlag now rejects names in BUILTIN_FLAG_NAMES with a clear error
(isolated per-extension by loadExtension's try/catch).
Adds tests for all three plus the documented startup-parse misclassification.
