Update your current angular dependencies to 1.3.x and add a resolution for angular to suppress the prompt:
{
"name": "myapp",
"version": "0.0.1",
"dependencies": {
"angular": "~1.3.x",
"angular-animate": "~1.3.x",
"angular-cookies": "~1.3.x",
"angular-resource": "~1.3.x",
"angular-sanitize": "~1.3.x",
"angular-ui-router": "~0.2.10",
"angular-ui-codemirror": "~0.1.6",
"angular-elastic": "~2.4.0",
"angular-local-storage": "~0.0.7",
"angular-nanoscroller": "~0.2.1",
"angular-sockjs": ">=0.0.1",
"json3": "~3.3.1",
"es5-shim": "~3.1.0",
"jquery": "~2.1.1",
"splitter": "*",
"chance": "~0.5.6",
"nanoscroller": "~0.8.4"
},
"resolutions": {
"angular": "~1.3.x"
}
}