A project override silently turns off presets for that template

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Issue 将 preset resolve 和预设文档列为切入点；阅读 artifact info 如何报告被隐藏的预设更改，并找到解释项目模板覆盖的文档。记录覆盖会隐藏预设更改；如果该行为属于范围内，则让 preset resolve 报告被隐藏的预设。完成标准是用户能够查明预设内容缺失的原因。

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描述

triage-can-wait

What happens (v1.2.6)
A team installs a preset that adds a section to the plan template. Later, a developer copies the plan template into .specify/templates/overrides/ to tweak one line. From then on, the preset's section is gone from every plan, and nothing says so:

  • specify preset resolve plan-template shows only the override.
  • specify preset list still shows the preset as enabled.
  • Only specify artifact info plan-template --kind template --json reveals it, as hidden: true.

This matches the rule that project overrides always win, so it isn't a bug. It's just invisible.

Reproduction script 
#!/usr/bin/env bash
# u5: a project override on a template silently drops every preset layer on it, and the CLI says nothing.
# A team preset that appends a section (the documented "append" strategy), plus a developer's own
# override of the same template (the documented .specify/templates/overrides/ folder). Stock CLI only.
set -uo pipefail
REF="${REF:-v1.2.6}"
WORK="$(mktemp -d)"
cd "$WORK"
SPECIFY=(uvx -q --from "git+https://github.com/github/spec-kit.git@$REF" specify)
"${SPECIFY[@]}" init --here --force --non-interactive --integration claude --script sh --ignore-agent-tools >/dev/null 2>&1 || { echo "init failed"; exit 2; }
echo "spec-kit $REF in $WORK"

mkdir -p preset-src/templates
cat > preset-src/preset.yml <<'YML'
schema_version: "1.0"
preset:
  id: "team-governance"
  name: "Team Governance"
  version: "0.1.0"
  description: "Appends a compliance appendix to every plan"
  author: "repro"
requires:
  speckit_version: ">=1.2.0"
provides:
  templates:
    - type: "template"
      name: "plan-template"
      file: "templates/plan-template.md"
      strategy: "append"
      description: "Compliance appendix appended to the plan"
tags: ["governance"]
YML
printf '\n## Compliance Appendix\n\nList every regulated data field the change touches.\n' > preset-src/templates/plan-template.md

echo "1. team installs the preset"
"${SPECIFY[@]}" preset add --dev ./preset-src </dev/null 2>&1 | tail -1
echo "   preset resolve plan-template:"
"${SPECIFY[@]}" preset resolve plan-template 2>&1 | sed 's/^/     /'

echo "2. a developer overrides the plan template for this project (copies it and edits a line)"
mkdir -p .specify/templates/overrides
sed 's/^# Implementation Plan/# Implementation Plan (our team)/' .specify/templates/plan-template.md > .specify/templates/overrides/plan-template.md
echo "   preset resolve plan-template:"
"${SPECIFY[@]}" preset resolve plan-template 2>&1 | sed 's/^/     /'
echo "   artifact info plan-template --kind template:"
"${SPECIFY[@]}" artifact info plan-template --kind template --json 2>&1 | python3 -c "import json,sys;d=json.load(sys.stdin);print(json.dumps(d,indent=1)[:1500])" 2>&1 | sed 's/^/     /'
echo "   preset list:"
"${SPECIFY[@]}" preset list 2>&1 | sed 's/^/     /' | head -8

o=.specify/templates/overrides/plan-template.md
if [ -f "$o" ] && [ "$(awk '/Compliance Appendix/{n++} END{print n+0}' "$o")" = "0" ]; then
  echo "RESULT: plan-template now resolves to $o, which has no Compliance Appendix. Read the output above for any warning that the preset is hidden."
fi

Suggested fix (small)

  1. One sentence in the presets docs: a project override replaces the template and hides every preset change to it.
  2. One line from preset resolve when that happens, for example "team-governance (append) is hidden by a project override". The information is already computed for artifact info, so this is a few lines. Happy to open a PR for it if that direction works for you.

AI disclosure: drafted with Claude Code (Claude Opus 5.5, default settings) from runs in a throwaway sandbox; I checked it before filing.

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