Shell scripts: paths-only validates branch and setup-plan can overwrite plan.md

[flamerged]

I found two shell-script behaviors in current main at 51e6a14 while vendoring Spec Kit into a repo and testing the generated Claude integration.

1. check-prerequisites.sh --paths-only still validates branch name

The help text says --paths-only should output path variables with no prerequisite validation. The Claude /speckit-clarify skill also calls:

.specify/scripts/bash/check-prerequisites.sh --json --paths-only

But check_feature_branch "$CURRENT_BRANCH" "$HAS_GIT" runs before the PATHS_ONLY early exit. In a normal non-Spec branch, --paths-only can fail before returning paths.

Suggested fix: move branch validation after the PATHS_ONLY block.

2. setup-plan.sh overwrites existing plan.md

setup-plan.sh unconditionally copies the plan template to $IMPL_PLAN:

cp "$TEMPLATE" "$IMPL_PLAN"

On reruns this can overwrite an already authored implementation plan.

Suggested fix: only copy/touch when $IMPL_PLAN does not exist, unless an explicit force mode is added. Also send status messages to stderr in --json mode so stdout remains parseable JSON.

I tested equivalent local patches in a temp Spec Kit directory:

• check-prerequisites.sh --json --paths-only returns JSON on a normal branch.
• setup-plan.sh --json preserves an existing plan.md.
• setup-plan.sh --json creates a missing plan.md and still emits parseable JSON.

[bixu]

Confirming this reproduces on current main: re-running /speckit-plan on a feature that already has a hand-authored plan.md silently replaces without warning.

The trigger in practice is the common "spec changed, re-plan" loop: run /speckit-clarify to record a decision, then /speckit-plan to propagate it — at which point the populated plan is lost. That overlaps with the workflow concern in #1059.

The suggested guard here (only cp when $IMPL_PLAN is absent, or behind an explicit --force) would prevent the data loss. Recovery via git checkout HEAD -- plan.md works, but only if the prior plan was already committed.