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.

scripts/bash/setup-plan.sh

@@ -40,15 +40,31 @@ fi
 # Ensure the feature directory exists
 mkdir -p "$FEATURE_DIR"
 
-# Copy plan template if it exists
-TEMPLATE=$(resolve_template "plan-template" "$REPO_ROOT") || true
-if [[ -n "$TEMPLATE" ]] && [[ -f "$TEMPLATE" ]]; then
-    cp "$TEMPLATE" "$IMPL_PLAN"
-    echo "Copied plan template to $IMPL_PLAN"
+# Copy plan template if plan doesn't already exist
+if [[ -f "$IMPL_PLAN" ]]; then
+    if $JSON_MODE; then
+        echo "Plan already exists at $IMPL_PLAN, skipping template copy" >&2
+    else
+        echo "Plan already exists at $IMPL_PLAN, skipping template copy"
+    fi
 else
-    echo "Warning: Plan template not found"
-    # Create a basic plan file if template doesn't exist
-    touch "$IMPL_PLAN"
+    TEMPLATE=$(resolve_template "plan-template" "$REPO_ROOT") || true
+    if [[ -n "$TEMPLATE" ]] && [[ -f "$TEMPLATE" ]]; then
+        cp "$TEMPLATE" "$IMPL_PLAN"
+        if $JSON_MODE; then
+            echo "Copied plan template to $IMPL_PLAN" >&2
+        else
+            echo "Copied plan template to $IMPL_PLAN"
+        fi
+    else
+        if $JSON_MODE; then
+            echo "Warning: Plan template not found" >&2
+        else
+            echo "Warning: Plan template not found"
+        fi
+        # Create a basic plan file if template doesn't exist
+        touch "$IMPL_PLAN"
+    fi
 fi
 
 # Output results