-stub before another option (not directly before the pipeline arg) resolves wrong pipeline (nextflow-io/true)

Bug report

Expected behavior and actual behavior

-stub/-stub-run, when immediately followed by another option (rather than
directly by the pipeline argument or the end of the command), causes Nextflow
to resolve the wrong pipeline: instead of pulling the given URL/name, it pulls
nextflow-io/true and fails with a "Remote resource not found" error.

Likely related to #3437 ("-stub-run as first option causes
failure"), filed in 2022 against 22.10.3 with the identical nextflow-io/true
symptom, which was auto-closed by stale-bot.

Steps to reproduce the problem

$ nextflow run -ansi-log false -stub -profile docker https://github.com/nf-core/fetchngs -r 0ae5518 -latest

vs. the same command with only -stub moved to the end:

$ nextflow run -ansi-log false -profile docker https://github.com/nf-core/fetchngs -r 0ae5518 -latest -stub

Also reproduces with a semver tag instead of a commit SHA (-r 1.12.0), with
-stub true (giving -stub an explicit value), and with the
short org/repo pipeline form, but not when -stub is immediately
followed directly by the pipeline argument itself.

Program output

Failing invocation:

Pulling nextflow-io/true:0ae5518 ...
WARN: Cannot read project manifest -- Cause: Remote resource not found: https://api.github.com/repos/nextflow-io/true/contents/nextflow.config?ref=0ae5518
Remote resource not found: https://api.github.com/repos/nextflow-io/true/contents/main.nf?ref=0ae5518

Same command with -stub moved after the pipeline argument:

Pulling nf-core/fetchngs:0ae5518 ...

Environment

• Nextflow version: 26.04.6.12646
• Java version: openjdk 17.0.20 2026-07-21
• Operating system: Debian GNU/Linux 12 (bookworm) — also confirmed on macOS
  with the same Nextflow version

Start by reproducing the failing and working nextflow run commands shown in the issue, then trace the command-line option parsing for -stub and pipeline arguments. Done means options before the pipeline no longer cause resolution to nextflow-io/true, while the shown URL, tag, commit, and short pipeline forms still resolve correctly.