fix: paths-only skips branch validation, setup-plan preserves existing plan (#2672)

* fix: paths-only skips branch validation, setup-plan preserves existing plan (#2653)

- check-prerequisites.sh/ps1: move branch validation after --paths-only
  early exit so --paths-only returns paths without requiring a spec branch
- setup-plan.sh/ps1: skip template copy when plan.md already exists to
  prevent overwriting user-authored plans on reruns
- setup-plan.sh: send status messages to stderr in --json mode so stdout
  remains parseable JSON
- Add tests for both fixes (bash + PowerShell)

* fix: remove trailing whitespace in PowerShell scripts

* fix: route PS skip message to stderr in -Json mode, add PS JSON assertions

Address review: setup-plan.ps1 Write-Output polluted stdout in -Json
mode when plan.md already existed. Use [Console]::Error.WriteLine()
when -Json is set. Add json.loads + stderr assertions to the PS rerun
test to catch regressions.

* fix: use Test-Path -PathType Leaf for plan existence check

Bare Test-Path matches directories too, which would silently skip plan
creation if a directory existed at the plan.md path.