feat(project-bootstrap): v1.3.0 — idempotent CLAUDE.md merge on upgrade

Step 5 was binary on upgrade (append whole template / leave alone), so
projects bootstrapped before v1.2.0 silently missed new canonical triggers
(`check across all projects`, `we're on Windows`) on re-run. Now upgrade
reads existing CLAUDE.md, substring-diffs vs template, preserves a
deliberately-pinned platform line, and appends only missing lines after
explicit confirm. Re-runs are no-ops.

Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>

skills/project-bootstrap/README.md

@@ -44,7 +44,7 @@ projects bootstrapped at different times debuggable.
 | `README.md` | minimal stub | Skipped if file exists. |
 | `.wiki/` | delegated to `setup-wiki` | Karpathy LLM Wiki layout — `CLAUDE.md`, `index.md`, `log.md`, `overview.md`, `raw/`, `entities/`, `concepts/`, `packages/`, `sources/`. |
 | `.tasks/` | delegated to `setup-tasks` | Canonical board — `STATUS.md` plus per-task `<task-slug>.md` files. |
-| `CLAUDE.md` | `assets/CLAUDE.md.template` | Skill triggers (`use superpowers`, `use project wiki`, etc.). On non-Windows hosts, swap the `we're on Windows` line for `we're on Linux` / `we're on macOS`. |
+| `CLAUDE.md` | `assets/CLAUDE.md.template` | Skill triggers (`use superpowers`, `use project wiki`, etc.). On non-Windows hosts, swap the `we're on Windows` line for `we're on Linux` / `we're on macOS`. On upgrade, the template is treated as a canonical set and merged idempotently — only missing trigger lines are appended after user confirm. Re-runs are no-ops. |
 | `.wiki/concepts/bootstrap-manifest.md` | generated | Records which skill versions initialized the project, so cross-project layout drift is debuggable. |
 
 ## Workflow

skills/project-bootstrap/SKILL.md

@@ -1,6 +1,6 @@
 ---
 name: project-bootstrap
-version: 1.2.0
+version: 1.3.0
 description: >
   Initializes or upgrades a project in the current folder: git, .gitignore, README.md,
   .wiki/ using Karpathy's method, .tasks/ for task tracking, CLAUDE.md with skill triggers.
@@ -219,12 +219,41 @@ If `setup-tasks` is not installed, **stop** and tell the user — same rule as S
 
 ## Step 5 — CLAUDE.md
 
-If `CLAUDE.md` already exists — show its contents and ask:
-"CLAUDE.md already exists. Append skill triggers to the end, or leave as is?"
+Two paths, picked by file presence:
 
-If it does not exist — create from template `assets/CLAUDE.md.template`.
+### Init (file does not exist)
+
+Create `CLAUDE.md` from `assets/CLAUDE.md.template`. Substitute the platform line
+on non-Windows hosts (`we're on Linux` / `we're on macOS` instead of
+`we're on Windows`).
+
+### Upgrade (file exists) — idempotent merge
+
+Treat the template as the canonical trigger set and reconcile the existing file
+against it. Re-runs are no-ops once the file is in canon.
+
+1. Read the existing `CLAUDE.md`.
+2. For each non-empty, non-comment line in the template, decide whether it's
+   already present:
+   - **Trigger lines** (everything except the platform line) — present iff any
+     existing line, after `trim` + `tolower`, contains the template line's
+     trigger text. Substring match, not equality — tolerates user rewording or
+     trailing punctuation.
+   - **Platform line** (`we're on Windows`) — present iff any existing line
+     matches `we're on (windows|linux|macos)` case-insensitively. If the user
+     pinned a different platform on purpose, **leave it alone**. Only append
+     the host-appropriate platform line when none of the three is present.
+3. Collect missing lines. If none → print `CLAUDE.md already canon — no changes`
+   and skip to Step 5.5.
+4. Show the user the diff (N lines, exact text to append) and ask one question:
+   "Append these N missing canonical triggers to the end of CLAUDE.md?" Wait
+   for explicit confirmation before writing.
+5. On confirm: append a single newline (if the file doesn't end with one) and
+   then the missing lines, one per line. Don't rewrite the file — only append.
+   Don't reorder existing lines. Don't dedupe within the existing file.
+
+Template contents (`assets/CLAUDE.md.template` — source of truth):
 
-Template contents:
 ```markdown
 # CLAUDE.md
 # Agent instructions. Each line is a trigger for an installed skill.