fix: use npm ci in bootstrap to prevent dirty lockfile blocking merges

setup.sh ran npm install which modified package-lock.json, causing
git merge to refuse during channel skill installation. Switch to
npm ci (deterministic, doesn't modify lockfile) and clean up stale
peer flags in the lockfile.

Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>

package-lock.json

@@ -1740,7 +1740,6 @@
       "integrity": "sha512-5gTmgEY/sqK6gFXLIsQNH19lWb4ebPDLA4SdLP7dsWkIXHWlG66oPuVvXSGFPppYZz8ZDZq0dYYrbHfBCVUb1Q==",
       "dev": true,
       "license": "MIT",
-      "peer": true,
       "engines": {
         "node": ">=12"
       },
@@ -2295,7 +2294,6 @@
       "integrity": "sha512-5C1sg4USs1lfG0GFb2RLXsdpXqBSEhAaA/0kPL01wxzpMqLILNxIxIOKiILz+cdg/pLnOUxFYOR5yhHU666wbw==",
       "dev": true,
       "license": "MIT",
-      "peer": true,
       "dependencies": {
         "esbuild": "~0.27.0",
         "get-tsconfig": "^4.7.5"
@@ -2355,7 +2353,6 @@
       "integrity": "sha512-w+N7Hifpc3gRjZ63vYBXA56dvvRlNWRczTdmCBBa+CotUzAPf5b7YMdMR/8CQoeYE5LX3W4wj6RYTgonm1b9DA==",
       "dev": true,
       "license": "MIT",
-      "peer": true,
       "dependencies": {
         "esbuild": "^0.27.0",
         "fdir": "^6.5.0",
@@ -2431,7 +2428,6 @@
       "integrity": "sha512-hOQuK7h0FGKgBAas7v0mSAsnvrIgAvWmRFjmzpJ7SwFHH3g1k2u37JtYwOwmEKhK6ZO3v9ggDBBm0La1LCK4uQ==",
       "dev": true,
       "license": "MIT",
-      "peer": true,
       "dependencies": {
         "@vitest/expect": "4.0.18",
         "@vitest/mocker": "4.0.18",
@@ -2532,7 +2528,6 @@
       "resolved": "https://registry.npmjs.org/yaml/-/yaml-2.8.2.tgz",
       "integrity": "sha512-mplynKqc1C2hTVYxd0PU2xQAc22TI1vShAYGksCCfxbn/dFwnHTNi1bvYsBTkhdUNtGIf5xNOg938rrSSYvS9A==",
       "license": "ISC",
-      "peer": true,
       "bin": {
         "yaml": "bin.mjs"
       },